7QW3 | pdb_00007qw3

R396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera in complex with Br ion.

PDB DOI: https://doi.org/10.2210/pdb7QW3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corallina pilulifera
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2022-01-24 Released: 2023-02-01
Deposition Author(s): Isupov, M.N., Mitchell, D., Littelchild, J.A., Garcia-Rodriguez, E.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.171 (Depositor), 0.171 (DCC)
R-Value Work:
0.143 (Depositor), 0.143 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7QW3

This is version 1.1 of the entry. See complete history.

Literature

R396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera

Isupov, M.N., Mitchell, D., Littelchild, J.A., Garcia-Rodriguez, E.

To be published.

Macromolecule Content

Total Structure Weight: 268.12 kDa
Atom Count: 23,528
Modeled Residue Count: 2,388
Deposited Residue Count: 2,392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vanadium-dependent bromoperoxidase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	598	Corallina pilulifera	Mutation(s): 0 EC: 1.11.1.18
UniProt
Find proteins for O81959 (Corallina pilulifera) Explore O81959 Go to UniProtKB: O81959
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O81959
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth BBB] SDF format, chain E [auth AAA] SDF format, chain G [auth AAA] SDF format, chain IB [auth DDD] SDF format, chain KB [auth DDD] SDF format, chain PA [auth CCC] SDF format, chain RA [auth CCC] SDF format, chain W [auth AAA] SDF format, chain Z [auth BBB] MOL2 format, chain BA [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain IB [auth DDD] MOL2 format, chain KB [auth DDD] MOL2 format, chain PA [auth CCC] MOL2 format, chain RA [auth CCC] MOL2 format, chain W [auth AAA] MOL2 format, chain Z [auth BBB] mmCIF format, chain BA [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain IB [auth DDD] mmCIF format, chain KB [auth DDD] mmCIF format, chain PA [auth CCC] mmCIF format, chain RA [auth CCC] mmCIF format, chain W [auth AAA] mmCIF format, chain Z [auth BBB]	BA [auth BBB] E [auth AAA] G [auth AAA] IB [auth DDD] KB [auth DDD] BA [auth BBB], E [auth AAA], G [auth AAA], IB [auth DDD], KB [auth DDD], PA [auth CCC], RA [auth CCC], W [auth AAA], Z [auth BBB]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth BBB] Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain IB [auth DDD] Focus chain KB [auth DDD] Focus chain PA [auth CCC] Focus chain RA [auth CCC] Focus chain W [auth AAA] Focus chain Z [auth BBB] Interactions & Density Focus chain BA [auth BBB] Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain IB [auth DDD] Focus chain KB [auth DDD] Focus chain PA [auth CCC] Focus chain RA [auth CCC] Focus chain W [auth AAA] Focus chain Z [auth BBB]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AB [auth CCC] SDF format, chain BB [auth CCC] SDF format, chain CB [auth CCC] SDF format, chain DB [auth CCC] SDF format, chain EB [auth CCC] SDF format, chain FA [auth BBB] SDF format, chain GA [auth BBB] SDF format, chain GB [auth CCC] SDF format, chain HA [auth BBB] SDF format, chain IA [auth BBB] SDF format, chain JA [auth BBB] SDF format, chain KA [auth BBB] SDF format, chain L [auth AAA] SDF format, chain LA [auth BBB] SDF format, chain M [auth AAA] SDF format, chain MA [auth BBB] SDF format, chain N [auth AAA] SDF format, chain O [auth AAA] SDF format, chain OB [auth DDD] SDF format, chain P [auth AAA] SDF format, chain PB [auth DDD] SDF format, chain Q [auth AAA] SDF format, chain QB [auth DDD] SDF format, chain R [auth AAA] SDF format, chain RB [auth DDD] SDF format, chain S [auth AAA] SDF format, chain SB [auth DDD] SDF format, chain T [auth AAA] SDF format, chain TB [auth DDD] SDF format, chain UB [auth DDD] SDF format, chain V [auth AAA] SDF format, chain VA [auth CCC] SDF format, chain VB [auth DDD] SDF format, chain WA [auth CCC] SDF format, chain WB [auth DDD] SDF format, chain XA [auth CCC] SDF format, chain XB [auth DDD] SDF format, chain YA [auth CCC] SDF format, chain ZA [auth CCC] MOL2 format, chain AB [auth CCC] MOL2 format, chain BB [auth CCC] MOL2 format, chain CB [auth CCC] MOL2 format, chain DB [auth CCC] MOL2 format, chain EB [auth CCC] MOL2 format, chain FA [auth BBB] MOL2 format, chain GA [auth BBB] MOL2 format, chain GB [auth CCC] MOL2 format, chain HA [auth BBB] MOL2 format, chain IA [auth BBB] MOL2 format, chain JA [auth BBB] MOL2 format, chain KA [auth BBB] MOL2 format, chain L [auth AAA] MOL2 format, chain LA [auth BBB] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth BBB] MOL2 format, chain N [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain OB [auth DDD] MOL2 format, chain P [auth AAA] MOL2 format, chain PB [auth DDD] MOL2 format, chain Q [auth AAA] MOL2 format, chain QB [auth DDD] MOL2 format, chain R [auth AAA] MOL2 format, chain RB [auth DDD] MOL2 format, chain S [auth AAA] MOL2 format, chain SB [auth DDD] MOL2 format, chain T [auth AAA] MOL2 format, chain TB [auth DDD] MOL2 format, chain UB [auth DDD] MOL2 format, chain V [auth AAA] MOL2 format, chain VA [auth CCC] MOL2 format, chain VB [auth DDD] MOL2 format, chain WA [auth CCC] MOL2 format, chain WB [auth DDD] MOL2 format, chain XA [auth CCC] MOL2 format, chain XB [auth DDD] MOL2 format, chain YA [auth CCC] MOL2 format, chain ZA [auth CCC] mmCIF format, chain AB [auth CCC] mmCIF format, chain BB [auth CCC] mmCIF format, chain CB [auth CCC] mmCIF format, chain DB [auth CCC] mmCIF format, chain EB [auth CCC] mmCIF format, chain FA [auth BBB] mmCIF format, chain GA [auth BBB] mmCIF format, chain GB [auth CCC] mmCIF format, chain HA [auth BBB] mmCIF format, chain IA [auth BBB] mmCIF format, chain JA [auth BBB] mmCIF format, chain KA [auth BBB] mmCIF format, chain L [auth AAA] mmCIF format, chain LA [auth BBB] mmCIF format, chain M [auth AAA] mmCIF format, chain MA [auth BBB] mmCIF format, chain N [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain OB [auth DDD] mmCIF format, chain P [auth AAA] mmCIF format, chain PB [auth DDD] mmCIF format, chain Q [auth AAA] mmCIF format, chain QB [auth DDD] mmCIF format, chain R [auth AAA] mmCIF format, chain RB [auth DDD] mmCIF format, chain S [auth AAA] mmCIF format, chain SB [auth DDD] mmCIF format, chain T [auth AAA] mmCIF format, chain TB [auth DDD] mmCIF format, chain UB [auth DDD] mmCIF format, chain V [auth AAA] mmCIF format, chain VA [auth CCC] mmCIF format, chain VB [auth DDD] mmCIF format, chain WA [auth CCC] mmCIF format, chain WB [auth DDD] mmCIF format, chain XA [auth CCC] mmCIF format, chain XB [auth DDD] mmCIF format, chain YA [auth CCC] mmCIF format, chain ZA [auth CCC]	AB [auth CCC] BB [auth CCC] CB [auth CCC] DB [auth CCC] EB [auth CCC] AB [auth CCC], BB [auth CCC], CB [auth CCC], DB [auth CCC], EB [auth CCC], FA [auth BBB], GA [auth BBB], GB [auth CCC], HA [auth BBB], IA [auth BBB], JA [auth BBB], KA [auth BBB], L [auth AAA], LA [auth BBB], M [auth AAA], MA [auth BBB], N [auth AAA], O [auth AAA], OB [auth DDD], P [auth AAA], PB [auth DDD], Q [auth AAA], QB [auth DDD], R [auth AAA], RB [auth DDD], S [auth AAA], SB [auth DDD], T [auth AAA], TB [auth DDD], UB [auth DDD], V [auth AAA], VA [auth CCC], VB [auth DDD], WA [auth CCC], WB [auth DDD], XA [auth CCC], XB [auth DDD], YA [auth CCC], ZA [auth CCC]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth CCC] Focus chain BB [auth CCC] Focus chain CB [auth CCC] Focus chain DB [auth CCC] Focus chain EB [auth CCC] Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain GB [auth CCC] Focus chain HA [auth BBB] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain OB [auth DDD] Focus chain P [auth AAA] Focus chain PB [auth DDD] Focus chain Q [auth AAA] Focus chain QB [auth DDD] Focus chain R [auth AAA] Focus chain RB [auth DDD] Focus chain S [auth AAA] Focus chain SB [auth DDD] Focus chain T [auth AAA] Focus chain TB [auth DDD] Focus chain UB [auth DDD] Focus chain V [auth AAA] Focus chain VA [auth CCC] Focus chain VB [auth DDD] Focus chain WA [auth CCC] Focus chain WB [auth DDD] Focus chain XA [auth CCC] Focus chain XB [auth DDD] Focus chain YA [auth CCC] Focus chain ZA [auth CCC] Interactions & Density Focus chain AB [auth CCC] Focus chain BB [auth CCC] Focus chain CB [auth CCC] Focus chain DB [auth CCC] Focus chain EB [auth CCC] Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain GB [auth CCC] Focus chain HA [auth BBB] Focus chain IA [auth BBB] Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain OB [auth DDD] Focus chain P [auth AAA] Focus chain PB [auth DDD] Focus chain Q [auth AAA] Focus chain QB [auth DDD] Focus chain R [auth AAA] Focus chain RB [auth DDD] Focus chain S [auth AAA] Focus chain SB [auth DDD] Focus chain T [auth AAA] Focus chain TB [auth DDD] Focus chain UB [auth DDD] Focus chain V [auth AAA] Focus chain VA [auth CCC] Focus chain VB [auth DDD] Focus chain WA [auth CCC] Focus chain WB [auth DDD] Focus chain XA [auth CCC] Focus chain XB [auth DDD] Focus chain YA [auth CCC] Focus chain ZA [auth CCC]
BR (Subject of Investigation/LOI) Query on BR Download:Ideal Coordinates CCD File SDF format, chain CA [auth BBB] SDF format, chain DA [auth BBB] SDF format, chain EA [auth BBB] SDF format, chain FB [auth CCC] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain K [auth AAA] SDF format, chain LB [auth DDD] SDF format, chain MB [auth DDD] SDF format, chain NA [auth BBB] SDF format, chain NB [auth DDD] SDF format, chain SA [auth CCC] SDF format, chain TA [auth CCC] SDF format, chain U [auth AAA] SDF format, chain UA [auth CCC] MOL2 format, chain CA [auth BBB] MOL2 format, chain DA [auth BBB] MOL2 format, chain EA [auth BBB] MOL2 format, chain FB [auth CCC] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain LB [auth DDD] MOL2 format, chain MB [auth DDD] MOL2 format, chain NA [auth BBB] MOL2 format, chain NB [auth DDD] MOL2 format, chain SA [auth CCC] MOL2 format, chain TA [auth CCC] MOL2 format, chain U [auth AAA] MOL2 format, chain UA [auth CCC] mmCIF format, chain CA [auth BBB] mmCIF format, chain DA [auth BBB] mmCIF format, chain EA [auth BBB] mmCIF format, chain FB [auth CCC] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain LB [auth DDD] mmCIF format, chain MB [auth DDD] mmCIF format, chain NA [auth BBB] mmCIF format, chain NB [auth DDD] mmCIF format, chain SA [auth CCC] mmCIF format, chain TA [auth CCC] mmCIF format, chain U [auth AAA] mmCIF format, chain UA [auth CCC]	CA [auth BBB] DA [auth BBB] EA [auth BBB] FB [auth CCC] H [auth AAA] CA [auth BBB], DA [auth BBB], EA [auth BBB], FB [auth CCC], H [auth AAA], I [auth AAA], J [auth AAA], K [auth AAA], LB [auth DDD], MB [auth DDD], NA [auth BBB], NB [auth DDD], SA [auth CCC], TA [auth CCC], U [auth AAA], UA [auth CCC]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain CA [auth BBB] Focus chain DA [auth BBB] Focus chain EA [auth BBB] Focus chain FB [auth CCC] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain LB [auth DDD] Focus chain MB [auth DDD] Focus chain NA [auth BBB] Focus chain NB [auth DDD] Focus chain SA [auth CCC] Focus chain TA [auth CCC] Focus chain U [auth AAA] Focus chain UA [auth CCC] Interactions & Density Focus chain CA [auth BBB] Focus chain DA [auth BBB] Focus chain EA [auth BBB] Focus chain FB [auth CCC] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain LB [auth DDD] Focus chain MB [auth DDD] Focus chain NA [auth BBB] Focus chain NB [auth DDD] Focus chain SA [auth CCC] Focus chain TA [auth CCC] Focus chain U [auth AAA] Focus chain UA [auth CCC]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain F [auth AAA] SDF format, chain JB [auth DDD] SDF format, chain QA [auth CCC] MOL2 format, chain AA [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain JB [auth DDD] MOL2 format, chain QA [auth CCC] mmCIF format, chain AA [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain JB [auth DDD] mmCIF format, chain QA [auth CCC]	AA [auth BBB], F [auth AAA], JB [auth DDD], QA [auth CCC]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth BBB] Focus chain F [auth AAA] Focus chain JB [auth DDD] Focus chain QA [auth CCC] Interactions & Density Focus chain AA [auth BBB] Focus chain F [auth AAA] Focus chain JB [auth DDD] Focus chain QA [auth CCC]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain HB [auth CCC] SDF format, chain OA [auth BBB] SDF format, chain X [auth AAA] SDF format, chain Y [auth AAA] SDF format, chain YB [auth DDD] MOL2 format, chain HB [auth CCC] MOL2 format, chain OA [auth BBB] MOL2 format, chain X [auth AAA] MOL2 format, chain Y [auth AAA] MOL2 format, chain YB [auth DDD] mmCIF format, chain HB [auth CCC] mmCIF format, chain OA [auth BBB] mmCIF format, chain X [auth AAA] mmCIF format, chain Y [auth AAA] mmCIF format, chain YB [auth DDD]	HB [auth CCC], OA [auth BBB], X [auth AAA], Y [auth AAA], YB [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HB [auth CCC] Focus chain OA [auth BBB] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain YB [auth DDD] Interactions & Density Focus chain HB [auth CCC] Focus chain OA [auth BBB] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain YB [auth DDD]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BYR Query on BYR	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	L-PEPTIDE LINKING	C₉ H₁₀ Br N O₃		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.171 (Depositor), 0.171 (DCC)
R-Value Work: 0.143 (Depositor), 0.143 (DCC)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.484	α = 90
b = 182.484	β = 90
c = 177.592	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
O	model building
Coot	model building
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-01

Deposition Author(s):

Littelchild, J.A.

Garcia-Rodriguez, E.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2023-02-01
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.