3CNL | pdb_00003cnl

Crystal structure of GNP-bound YlqF from T. maritima

PDB DOI: https://doi.org/10.2210/pdb3CNL/pdb

Classification: SIGNALING PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-26 Released: 2008-06-24
Deposition Author(s): Kim, D.J., Jang, J.Y., Yoon, H.-J., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.284 (Depositor), 0.258 (DCC)
R-Value Work:
0.227 (Depositor)
R-Value Observed:
0.233 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of YlqF, a circularly permuted GTPase: Implications for its GTPase activation in 50 S ribosomal subunit assembly

Kim, D.J., Jang, J.Y., Yoon, H.-J., Suh, S.W.

(2008) Proteins 72: 1363-1370

PubMed: 18536017 Search on PubMed
DOI: https://doi.org/10.1002/prot.22112
Primary Citation Related Structures:
3CNL, 3CNN, 3CNO

Organizational Affiliation

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

Macromolecule Content

Total Structure Weight: 30.16 kDa
Atom Count: 2,032
Modeled Residue Count: 233
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	262	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_0768
UniProt
Find proteins for Q9WZM6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZM6 Go to UniProtKB: Q9WZM6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP 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]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		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: 0.284 (Depositor), 0.258 (DCC)
R-Value Work: 0.227 (Depositor)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.132	α = 90
b = 75.15	β = 90
c = 104.919	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.