3MSQ | pdb_00003msq

Crystal structure of a Putative ubiquinone biosynthesis protein (Npun02000094) from Nostoc punctiforme PCC 73102 at 2.85 A resolution

PDB DOI: https://doi.org/10.2210/pdb3MSQ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Nostoc punctiforme PCC 73102
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-04-29 Released: 2010-08-04
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.223 (Depositor), 0.240 (DCC)
R-Value Work:
0.195 (Depositor), 0.210 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a Putative ubiquinone biosynthesis protein (Npun02000094) from Nostoc punctiforme PCC 73102 at 2.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 103.16 kDa
Atom Count: 6,552
Modeled Residue Count: 828
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ubiquinone biosynthesis protein	A, B, C, D	224	Nostoc punctiforme PCC 73102	Mutation(s): 0 Gene Names: 23130561, Npun_R0350
UniProt
Find proteins for B2J5W7 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J5W7 Go to UniProtKB: B2J5W7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2J5W7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.223 (Depositor), 0.240 (DCC)
R-Value Work: 0.195 (Depositor), 0.210 (DCC)
R-Value Observed: 0.197 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33MSQ

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.72	α = 90
b = 82.03	β = 90
c = 187.64	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PHENIX	refinement
SHELX	phasing
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-16
Changes: Data collection, 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.