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- PDB-1tzf: X-ray Crystal Structure of alpha-D-glucose-1-phosphate cytidylylt... -

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Basic information

Entry
Database: PDB / ID: 1tzf
TitleX-ray Crystal Structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi
ComponentsGlucose-1-phosphate cytidylyltransferase
KeywordsTRANSFERASE / nucleotidyltransferase / mixed alpha/beta fold
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
Chem-C5G / Glucose-1-phosphate cytidylyltransferase / Glucose-1-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKoropatkin, N.M. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi
Authors: Koropatkin, N.M. / Holden, H.M.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

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Assembly

Deposited unit
A: Glucose-1-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7933
Polymers29,2041
Non-polymers5902
Water2,918162
1
A: Glucose-1-phosphate cytidylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)178,75918
Polymers175,2226
Non-polymers3,53812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area22980 Å2
ΔGint-216 kcal/mol
Surface area58960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.500, 88.500, 162.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

DetailsThe biological unit is a hexamer, generated from the monomer in the asymmetric unit by the operations: ROTATION MATRIX: -0.50000 -0.86603 0.00000 0.86603 -0.50000 0.00001 -0.00001 0.00000 1.00000 TRANSLATION VECTOR IN AS 0.00043 0.00017 0.00008 ROTATION MATRIX: -0.50000 0.86602 0.00000 -0.86602 -0.50000 0.00000 0.00000 0.00000 1.00000 TRANSLATION VECTOR IN AS 0.00046 0.00027 0.00009 ROTATION MATRIX: -1.00000 0.00000 0.00000 0.00000 1.00000 0.00001 0.00000 0.00001 -1.00000 TRANSLATION VECTOR IN AS 0.00020 -0.00001 81.14987 ROTATION MATRIX: 0.50000 0.86602 0.00000 0.86602 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS 0.00082 0.00015 81.15000 ROTATION MATRIX: 0.50000 -0.86603 0.00000 -0.86603 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS 0.00045 0.00058 81.14999 These are the rotation and translation operations to be performed on the original monomer to generate the next five subunits of the complete hexamer 'P 63 2 2' 1 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 'P 63 2 2' 3 0 -1 0 1 -1 0 0 0 1 0 0 0 0 0 0 'P 63 2 2' 5 -1 1 0 -1 0 0 0 0 1 0 0 0 0 0 0 'P 63 2 2' 7 1 -1 0 0 -1 0 0 0 -1 0 0 0 0 0 0 'P 63 2 2' 9 -1 0 0 -1 1 0 0 0 -1 0 0 0 0 0 0 'P 63 2 2' 11 0 1 0 1 0 0 0 0 -1 0 0 0 0 0 0 'P 63 2 2' 2 1 -1 0 1 0 0 0 0 1 0 0 0 0 1 2 'P 63 2 2' 4 -1 0 0 0 -1 0 0 0 1 0 0 0 0 1 2 'P 63 2 2' 6 0 1 0 -1 1 0 0 0 1 0 0 0 0 1 2 'P 63 2 2' 8 0 -1 0 -1 0 0 0 0 -1 0 0 0 0 1 2 'P 63 2 2' 10 -1 1 0 0 1 0 0 0 -1 0 0 0 0 1 2 'P 63 2 2' 12 1 0 0 1 -1 0 0 0 -1 0 0 0 0 1 2

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Components

#1: Protein Glucose-1-phosphate cytidylyltransferase / E.C.2.7.7.33 / 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
Details: complexed with cytidyl-5'-phosphate-glucosyl-6-phosphate
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Species: Salmonella enterica / Strain: CT18 / Gene: rfbF / Plasmid: pET28a / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-C5G / [CYTIDINE-5'-PHOSPHATE]-BETA-GLUCOSYL-PHOSPHORIC ACID ESTER


Mass: 565.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N3O16P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, Ammonium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9641 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 29, 2004
RadiationMonochromator: Double crystal Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 22401 / Num. obs: 22358 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rsym value: 0.067 / Net I/σ(I): 65.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 9.9 / Num. unique all: 2163 / Rsym value: 0.176 / % possible all: 98.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
TNTrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2238 5 %random
Rwork0.197 ---
all0.199 22358 --
obs0.199 22358 --
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 37 162 2188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d18.2

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