8GRZ | pdb_00008grz

X-ray crystal structure of V71C human neuroglobin mutant

PDB DOI: https://doi.org/10.2210/pdb8GRZ/pdb

Classification: OXYGEN STORAGE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-09-03 Released: 2023-09-06
Deposition Author(s): Lin, Y.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-ray crystal structure of V71C human neuroglobin mutant

Lin, Y.W.

To be published.

Macromolecule Content

Total Structure Weight: 17.57 kDa
Atom Count: 1,287
Modeled Residue Count: 147
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroglobin	A	151	Homo sapiens	Mutation(s): 1 Gene Names: NGB EC: 1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPG2 (Homo sapiens) Explore Q9NPG2 Go to UniProtKB: Q9NPG2
PHAROS: Q9NPG2 GTEx: ENSG00000165553
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPG2
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: 2.00 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.497	α = 90
b = 39.553	β = 120.318
c = 48.858	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-09-06
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

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.