4Q8B | pdb_00004q8b

The crystal structure of CotA laccase complexed with sinapic acid

PDB DOI: https://doi.org/10.2210/pdb4Q8B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-04-26 Released: 2015-04-29
Deposition Author(s): Xie, T., Liu, Z.C., Wang, G.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.186 (Depositor), 0.198 (DCC)
R-Value Work:
0.139 (Depositor)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of CotA laccase complexed with sinapic acid

Xie, T., Liu, Z.C., Wang, G.G.

To be published.

Macromolecule Content

Total Structure Weight: 118.29 kDa
Atom Count: 8,985
Modeled Residue Count: 998
Deposited Residue Count: 1,026
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spore coat protein A	A, B	513	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: cotA, pig, BSU06300 EC: 1.10.3.2 (UniProt), 1.3.3.5 (UniProt)
UniProt
Find proteins for P07788 (Bacillus subtilis (strain 168)) Explore P07788 Go to UniProtKB: P07788
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SXX Query on SXX Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	SINAPINATE C₁₁ H₁₂ O₅ PCMORTLOPMLEFB-ONEGZZNKSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] M [auth B] C [auth A], D [auth A], E [auth A], F [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	H [auth A], I [auth A], J [auth A], S [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.186 (Depositor), 0.198 (DCC)
R-Value Work: 0.139 (Depositor)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.278	α = 90
b = 116.612	β = 99.32
c = 81.099	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-04-29

Deposition Author(s):

Xie, T.

Liu, Z.C.

Wang, G.G.

Revision History (Full details and data files)

Version 1.0: 2015-04-29
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary