4HO8 | pdb_00004ho8

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-glucose and thymidine

PDB DOI: https://doi.org/10.2210/pdb4HO8/pdb

Classification: TRANSFERASE
Organism(s): Aneurinibacillus thermoaerophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-22 Released: 2013-10-23
Deposition Author(s): Chen, T.J., Chien, W.T., Lin, C.C., Wang, W.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.240 (Depositor), 0.184 (DCC)
R-Value Work:
0.185 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-glucose and thymidine

Chen, T.J., Chien, W.T., Lin, C.C., Wang, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 136.47 kDa
Atom Count: 9,462
Modeled Residue Count: 1,152
Deposited Residue Count: 1,188
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A, B, C, D	297	Aneurinibacillus thermoaerophilus	Mutation(s): 0 Gene Names: rmlA EC: 2.7.7.24
UniProt
Find proteins for Q9AGY4 (Aneurinibacillus thermoaerophilus) Explore Q9AGY4 Go to UniProtKB: Q9AGY4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9AGY4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG Query on UPG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain V [auth D] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth D] mmCIF format, chain E [auth A]	E [auth A], J [auth B], P [auth C], V [auth D]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D]
THM Query on THM Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D]	F [auth A], K [auth B], Q [auth C], W [auth D]	THYMIDINE C₁₀ H₁₄ N₂ O₅ IQFYYKKMVGJFEH-XLPZGREQSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain X [auth D] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth D] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth D] mmCIF format, chain L [auth B]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.240 (Depositor), 0.184 (DCC)
R-Value Work: 0.185 (Depositor), 0.187 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.016	α = 90
b = 91.25	β = 90.13
c = 91.233	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description