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- PDB-1wvc: alpha-D-glucose-1-phosphate cytidylyltransferase complexed with CTP -

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Basic information

Entry
Database: PDB / ID: 1wvc
Titlealpha-D-glucose-1-phosphate cytidylyltransferase complexed with CTP
ComponentsGlucose-1-phosphate cytidylyltransferase
KeywordsTRANSFERASE / CDP-glucose pyrophosphorylase / nucleotidyltransferase
Function / homology
Function and homology information


glucose-1-phosphate cytidylyltransferase / glucose-1-phosphate cytidylyltransferase activity / O antigen biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Glucose-1-phosphate cytidylyltransferase / : / 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
CYTIDINE-5'-TRIPHOSPHATE / NICKEL (II) ION / Glucose-1-phosphate cytidylyltransferase / Glucose-1-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKoropatkin, N.M. / Cleland, W.W. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
Authors: Koropatkin, N.M. / Cleland, W.W. / Holden, H.M.
History
DepositionDec 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7945
Polymers29,2041
Non-polymers5904
Water1,63991
1
A: Glucose-1-phosphate cytidylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)178,76430
Polymers175,2226
Non-polymers3,54324
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area23540 Å2
ΔGint-252 kcal/mol
Surface area60470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.2, 84.2, 157.4
Angle α, β, γ (deg.)90, 90, 120
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Glucose-1-phosphate cytidylyltransferase / alpha-D-glucose-1-phosphate cytidylyltransferase / CDP-glucose pyrophosphorylase


Mass: 29203.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Species: Salmonella enterica / Strain: CT18 / Gene: rfbF / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P26396, UniProt: Q8Z5I4*PLUS, glucose-1-phosphate cytidylyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, magnesium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9641 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 11780 / Num. obs: 11780 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rsym value: 0.062 / Net I/σ(I): 26.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1064 / Rsym value: 0.274 / % possible all: 90.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
TNTrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TZF

1tzf


Resolution: 2.5→25 Å / σ(F): 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1123 -random
Rwork0.199 ---
all0.202 11746 --
obs0.202 11746 97.4 %-
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 32 91 2119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d20
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.2

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