6VZ6 | pdb_00006vz6

Methanococcoides burtonii cytochrome b5 domain protein (WP 011499504.1)

PDB DOI: https://doi.org/10.2210/pdb6VZ6/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Methanococcoides burtonii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-27 Released: 2020-03-11
Deposition Author(s): Teakel, S.L., Forwood, J.K., Aragao, D., Cahill, M.A., Marama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.195 (Depositor), 0.196 (DCC)
R-Value Work:
0.162 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Methanococcoides burtonii cytochrome b5 domain protein (WP 011499504.1)

Teakel, S.L., Forwood, J.K., Aragao, D., Cahill, M.A., Marama, M.

To be published.

Macromolecule Content

Total Structure Weight: 9.38 kDa
Atom Count: 726
Modeled Residue Count: 77
Deposited Residue Count: 78
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b5-domain protein	A	78	Methanococcoides burtonii	Mutation(s): 0
UniProt
Find proteins for Q12W16 (Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 / ACE-M)) Explore Q12W16 Go to UniProtKB: Q12W16
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12W16
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 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: 2.10 Å
R-Value Free: 0.195 (Depositor), 0.196 (DCC)
R-Value Work: 0.162 (Depositor), 0.163 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.495	α = 90
b = 67.495	β = 90
c = 48.132	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-03-11
Type: Initial release
Version 1.1: 2023-03-29
Changes: Database references, Structure summary
Version 1.2: 2023-10-25
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.