5KDB

The crystal structure of 4-isopropylbenzoate-bound CYP199A4

PDB DOI: https://doi.org/10.2210/pdb5KDB/pdb

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

Deposited: 2016-06-07 Released: 2018-02-07
Deposition Author(s): Coleman, T., Bruning, J.B., Bell, S.G.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 ?
R-Value Free: 0.186
R-Value Work: 0.147
R-Value Observed: 0.148

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The crystal structure of 4-isopropylbenzoate-bound CYP199A4

Coleman, T., Bruning, J.B., Bell, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 43.71 kDa
Atom Count: 3,566
Modelled Residue Count: 393
Deposited Residue Count: 393
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	393	Rhodopseudomonas palustris HaA2	Mutation(s): 0 Gene Names: RPB_3613
UniProt
Find proteins for Q2IU02 (Rhodopseudomonas palustris (strain HaA2)) Explore Q2IU02 Go to UniProtKB: Q2IU02
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
4IA Query on 4IA 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]	4-propan-2-ylbenzoic acid C₁₀ H₁₂ O₂ CKMXAIVXVKGGFM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [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: 1.64 ?
R-Value Free: 0.186
R-Value Work: 0.147
R-Value Observed: 0.148
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 44.313	α = 90
b = 51.453	β = 91.88
c = 79.283	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-07

Deposition Author(s):

Coleman, T.

Bruning, J.B.

Bell, S.G.

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

Revision History (Full details and data files)

Version 1.0: 2018-02-07
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description

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5KDB

The crystal structure of 4-isopropylbenzoate-bound CYP199A4

The crystal structure of 4-isopropylbenzoate-bound CYP199A4

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)