7X53 | pdb_00007x53

cytochrome P450 monooxygenase

PDB DOI: https://doi.org/10.2210/pdb7X53/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-03-03 Released: 2023-03-08
Deposition Author(s): Yan, Y., Zheng, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.321 (Depositor), 0.320 (DCC)
R-Value Work:
0.270 (Depositor), 0.270 (DCC)
R-Value Observed:
0.272 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7X53

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of cytochrome P450 monooxygenase at 3.35 Angstroms resolution.

Yan, Y., Zheng, C., Wei, S., Jing, W., Liang, G., Cong, G., Jia, L., Xiulai, C., Liming, L.

To be published.

Macromolecule Content

Total Structure Weight: 94.27 kDa
Atom Count: 6,550
Modeled Residue Count: 812
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 family protein	A, B	411	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: PP_1955
UniProt
Find proteins for Q88LH7 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88LH7 Go to UniProtKB: Q88LH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88LH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.321 (Depositor), 0.320 (DCC)
R-Value Work: 0.270 (Depositor), 0.270 (DCC)
R-Value Observed: 0.272 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.831	α = 90
b = 55.63	β = 102.94
c = 88.023	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2024-05-29
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.