5WCP

Phosphotriesterase variant S7

PDB DOI: https://doi.org/10.2210/pdb5WCP/pdb

Classification: HYDROLASE
Organism(s): Brevundimonas diminuta
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-07-01 Released: 2019-01-23
Deposition Author(s): Miton, C.M., Campbell, E.C., Jackson, C.J., Tokuriki, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175
R-Value Work: 0.151
R-Value Observed: 0.153

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Phosphotriesterase variant S7

Miton, C.M., Campbell, E.C., Jackson, C.J., Tokuriki, N.

To be published.

Macromolecule Content

Total Structure Weight: 72.73 kDa
Atom Count: 5,653
Modelled Residue Count: 628
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase	A, B [auth G]	333	Brevundimonas diminuta	Mutation(s): 0
UniProt
Find proteins for A0A060GZX0 (Brevundimonas diminuta) Explore A0A060GZX0 Go to UniProtKB: A0A060GZX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A060GZX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth G] MOL2 format, chain E [auth A] MOL2 format, chain L [auth G] mmCIF format, chain E [auth A] mmCIF format, chain L [auth G]	E [auth A], L [auth G]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth G] Interactions & Density Focus chain E [auth A] Focus chain L [auth G]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth G] SDF format, chain N [auth G] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth G] mmCIF format, chain N [auth G]	F [auth A] G [auth A] H [auth A] I [auth A] M [auth G] F [auth A], G [auth A], H [auth A], I [auth A], M [auth G], N [auth G]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth G] Focus chain N [auth G] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth G] Focus chain N [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth G] SDF format, chain K [auth G] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth G] mmCIF format, chain K [auth G]	C [auth A], D [auth A], J [auth G], K [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth G] Focus chain K [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B [auth G]	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175
R-Value Work: 0.151
R-Value Observed: 0.153
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.598	α = 90
b = 85.954	β = 90
c = 88.443	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2023-04-26
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection