8AA7 | pdb_00008aa7

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme coordinated fragment

PDB DOI: https://doi.org/10.2210/pdb8AA7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-30 Released: 2023-07-12
Deposition Author(s): Snee, M., Katariya, M., Levy, C., Leys, D.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.225 (Depositor), 0.224 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme coordinated fragment

Snee, M., Katariya, M.

To be published.

Macromolecule Content

Total Structure Weight: 46.76 kDa
Atom Count: 3,552
Modeled Residue Count: 394
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 protein	A	400	Staphylococcus aureus	Mutation(s): 0 Gene Names: cypX_1, NCTC5664_01270, cypX EC: 1.14.15.13 (PDB Primary Data), 1.14 (UniProt)
UniProt
Find proteins for A0A380DQV1 (Staphylococcus aureus) Explore A0A380DQV1 Go to UniProtKB: A0A380DQV1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A380DQV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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]
WYH (Subject of Investigation/LOI) Query on WYH 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]	2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole C₁₁ H₁₂ N₂ CFTOTSJVQRFXOF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.225 (Depositor), 0.224 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.241	α = 90
b = 106.412	β = 90
c = 105.677	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-12

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-07-12
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.