2ASH | pdb_00002ash

Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb2ASH/pdb

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

Deposited: 2005-08-23 Released: 2005-09-06
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine (tm1561) from THERMOTOGA MARITIMA at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 172.84 kDa
Atom Count: 11,856
Modeled Residue Count: 1,443
Deposited Residue Count: 1,524
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A, B, C, D	381	Thermotoga maritima	Mutation(s): 0 Gene Names: tgt EC: 2.4.2.29
UniProt
Find proteins for Q9X1P7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1P7 Go to UniProtKB: Q9X1P7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1P7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], M [auth C], T [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain T [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] L [auth B] P [auth C] H [auth A], I [auth A], J [auth A], L [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], V [auth D], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], N [auth C], O [auth C], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.229 (Depositor), 0.229 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.467	α = 90
b = 99.422	β = 123.8
c = 124.163	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-09-06

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-09-06
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description

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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.