1LVW | pdb_00001lvw

Crystal structure of glucose-1-phosphate thymidylyltransferase, RmlA, complex with dTDP

PDB DOI: https://doi.org/10.2210/pdb1LVW/pdb

Classification: TRANSFERASE
Organism(s): Methanothermobacter thermautotrophicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-05-29 Released: 2003-07-29
Deposition Author(s): Dong, A., Christendat, D., Pai, E.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.215 (Depositor), 0.210 (DCC)
R-Value Work:
0.187 (Depositor), 0.180 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of glucose-1-phosphate thymidylyltransferase, RmlA, complex with dTDP

Dong, A., Christendat, D., Pai, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 138.06 kDa
Atom Count: 10,472
Modeled Residue Count: 1,170
Deposited Residue Count: 1,180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucose-1-phosphate thymidylyltransferase	A, B, C, D	295	Methanothermobacter thermautotrophicus	Mutation(s): 0 Gene Names: RMLA EC: 2.7.7.24
UniProt
Find proteins for O27819 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27819 Go to UniProtKB: O27819
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O27819
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TYD Query on TYD Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	AA [auth D] BA [auth D] G [auth A] H [auth A] M [auth B] AA [auth D], BA [auth D], G [auth A], H [auth A], M [auth B], N [auth B], T [auth C], U [auth C]	THYMIDINE-5'-DIPHOSPHATE C₁₀ H₁₆ N₂ O₁₁ P₂ UJLXYODCHAELLY-XLPZGREQSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain F [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain F [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain F [auth A]	F [auth A], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth D] SDF format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D]	CA [auth D] DA [auth D] I [auth A] J [auth A] K [auth A] CA [auth D], DA [auth D], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B], R [auth C], S [auth C], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.215 (Depositor), 0.210 (DCC)
R-Value Work: 0.187 (Depositor), 0.180 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.68	α = 90
b = 115.88	β = 90
c = 116.91	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-07-29

Deposition Author(s):

Dong, A.

Christendat, D.

Pai, E.F.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2003-07-29
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations