7JW5 | pdb_00007jw5

Crystal structure of WT-CYP199A4 in complex with 4-phenylbenzoic acid

PDB DOI: https://doi.org/10.2210/pdb7JW5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodopseudomonas palustris HaA2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-24 Released: 2021-09-01
Deposition Author(s): Lee, J.H.Z., Bruning, J.B., Bell, S.G.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.198 (Depositor), 0.200 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Different Geometric Requirements for Cytochrome P450-Catalyzed Aliphatic Versus Aromatic Hydroxylation Results in Chemoselective Oxidation

Coleman, T., Kirk, A.M., Lee, J.H.Z., Doherty, D.Z., Bruning, J.B., Krenske, E.H., De Voss, J.J., Bell, S.G.

(2022) ACS Catal 12: 1258-1267

DOI: https://doi.org/10.1021/acscatal.1c05483

Macromolecule Content

Total Structure Weight: 45.44 kDa
Atom Count: 3,514
Modeled Residue Count: 393
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	410	Rhodopseudomonas palustris HaA2	Mutation(s): 0 Gene Names: RPB_3613 EC: 1
UniProt
Find proteins for Q2IU02 (Rhodopseudomonas palustris (strain HaA2)) Explore Q2IU02 Go to UniProtKB: Q2IU02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2IU02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
Z7Z (Subject of Investigation/LOI) Query on Z7Z Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	biphenyl-4-carboxylic acid C₁₃ H₁₀ O₂ NNJMFJSKMRYHSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.198 (Depositor), 0.200 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.513	α = 90
b = 51.486	β = 92.14
c = 78.725	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP140103229

Revision History (Full details and data files)

Version 1.0: 2021-09-01
Type: Initial release
Version 1.1: 2022-03-16
Changes: Database references
Version 1.2: 2023-10-18
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.