3IC6 | pdb_00003ic6

Crystal structure of putative methylase family protein from Neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb3IC6/pdb

Classification: structural genomics, unknown function
Organism(s): Neisseria gonorrhoeae FA 1090
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-07-17 Released: 2009-08-04
Deposition Author(s): Chang, C., Marshall, N., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.244 (Depositor), 0.249 (DCC)
R-Value Work:
0.209 (Depositor), 0.219 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative methylase family protein from Neisseria gonorrhoeae

Chang, C., Marshall, N., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 24.69 kDa
Atom Count: 1,653
Modeled Residue Count: 213
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methylase family protein	A	223	Neisseria gonorrhoeae FA 1090	Mutation(s): 0 Gene Names: NGO0670
UniProt
Find proteins for Q5F8U0 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F8U0 Go to UniProtKB: Q5F8U0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5F8U0
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: 2.59 Å
R-Value Free: 0.244 (Depositor), 0.249 (DCC)
R-Value Work: 0.209 (Depositor), 0.219 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.123	α = 90
b = 73.123	β = 90
c = 193.315	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
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.