3B4X | pdb_00003b4x

Crystal Structure Analysis of Sulfolobus tokodaii strain7 cytochrom P450

PDB DOI: https://doi.org/10.2210/pdb3B4X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sulfurisphaera tokodaii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-10-24 Released: 2008-11-04
Deposition Author(s): Kamitori, S., Yoshida, H., Ohtaki, A., Nakamura, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.219 (Depositor), 0.204 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Monooxygenation by Thermophilic Cytochrome P450 via Direct Electron Transfer from NADH without Redox Partner

Matsumura, H., Nakamura, N., Ohtaki, A., Yoshida, H., Kamitori, S., Yohda, M., Ohno, H.

To be published.

Macromolecule Content

Total Structure Weight: 43.03 kDa
Atom Count: 3,113
Modeled Residue Count: 367
Deposited Residue Count: 367
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
367aa long hypothetical cytochrome P450	A	367	Sulfurisphaera tokodaii	Mutation(s): 1 Gene Names: ST1148 EC: 1.14.14.1 (PDB Primary Data), 1.14 (UniProt)
UniProt
Find proteins for Q972I2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q972I2 Go to UniProtKB: Q972I2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q972I2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.219 (Depositor), 0.204 (DCC)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.286	α = 90
b = 55.168	β = 93.85
c = 51.415	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
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.