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- PDB-1lvw: Crystal structure of glucose-1-phosphate thymidylyltransferase, R... -

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Basic information

Entry
Database: PDB / ID: 1lvw
TitleCrystal structure of glucose-1-phosphate thymidylyltransferase, RmlA, complex with dTDP
Componentsglucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / protein nucleotide complex / nucleotide binding fold / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / :
Similarity search - Function
Glucose-1-phosphate thymidylyltransferase, short form / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsDong, A. / Christendat, D. / Pai, E.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of glucose-1-phosphate thymidylyltransferase, RmlA, complex with dTDP
Authors: Dong, A. / Christendat, D. / Pai, E.F.
History
DepositionMay 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glucose-1-phosphate thymidylyltransferase
B: glucose-1-phosphate thymidylyltransferase
C: glucose-1-phosphate thymidylyltransferase
D: glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,06430
Polymers133,4644
Non-polymers4,60026
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23790 Å2
ΔGint-201 kcal/mol
Surface area41700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.680, 115.880, 116.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer; two dimers in asymmetric unit

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
glucose-1-phosphate thymidylyltransferase


Mass: 33366.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: RMLA / Plasmid: pet15b / Production host: Escherichia coli (E. coli)
References: UniProt: O27819, glucose-1-phosphate thymidylyltransferase

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Non-polymers , 5 types, 769 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate, 24% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.0719, 1.0726, 1.0455
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07191
21.07261
31.04551
ReflectionResolution: 1.7→35 Å / Num. all: 162038 / Num. obs: 161361 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.15 % / Rsym value: 0.048 / Net I/σ(I): 19.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.279 / % possible all: 71.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→31.52 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 8072 4.8 %random
Rwork0.187 ---
all-162038 --
obs-161115 95.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9278 0 281 743 10302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.6
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d23.7
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.1
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 1.7→1.71 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.292 102
Rwork0.287 2120

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