3MZY | pdb_00003mzy

The Crystal Structure of the RNA polymerase sigma-H factor from Fusobacterium nucleatum to 2.5A

PDB DOI: https://doi.org/10.2210/pdb3MZY/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-13 Released: 2010-06-02
Deposition Author(s): Stein, A.J., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.269 (Depositor), 0.266 (DCC)
R-Value Work:
0.234 (Depositor), 0.229 (DCC)
R-Value Observed:
0.236 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of the RNA polymerase sigma-H factor from Fusobacterium nucleatum to 2.5A

Stein, A.J., Chhor, G., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 19.36 kDa
Atom Count: 983
Modeled Residue Count: 123
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma-H factor	A	164	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: FN1518
UniProt
Find proteins for Q8RIQ2 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RIQ2 Go to UniProtKB: Q8RIQ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RIQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.269 (Depositor), 0.266 (DCC)
R-Value Work: 0.234 (Depositor), 0.229 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.761	α = 90
b = 71.761	β = 90
c = 153.623	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-06-02
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: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.