3HRL | pdb_00003hrl

Crystal structure of a putative endonuclease-like protein (ngo0050) from neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb3HRL/pdb

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

Deposited: 2009-06-09 Released: 2009-06-30
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Cobb, G., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.226 (Depositor), 0.268 (DCC)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3HRL

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

Literature

Crystal Structure of a Putative Endonuclease-Like Protein (Ngo0050) from Neisseria Gonorrhoeae

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Cobb, G., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 12.25 kDa
Atom Count: 881
Modeled Residue Count: 94
Deposited Residue Count: 104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease-Like Protein	A	104	Neisseria gonorrhoeae FA 1090	Mutation(s): 0 Gene Names: NGO0050
UniProt
Find proteins for Q5FAH0 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5FAH0 Go to UniProtKB: Q5FAH0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5FAH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.95 Å
R-Value Free: 0.226 (Depositor), 0.268 (DCC)
R-Value Work: 0.183 (Depositor)
R-Value Observed: 0.185 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.922	α = 90
b = 52.922	β = 90
c = 102.295	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-06
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.