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- PDB-2b7l: Crystal Structure of CTP:Glycerol-3-Phosphate Cytidylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 2b7l
TitleCrystal Structure of CTP:Glycerol-3-Phosphate Cytidylyltransferase from Staphylococcus aureus
Componentsglycerol-3-phosphate cytidylyltransferase
KeywordsTRANSFERASE / cytidylyltransferase / Rossmann fold
Function / homology
Function and homology information


glycerol-3-phosphate cytidylyltransferase / glycerol-3-phosphate cytidylyltransferase activity / teichoic acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Glycerol-3-phosphate cytidylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycerol-3-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFong, D.H. / Yim, V.C.-N. / D'Elia, M.A. / Brown, E.D. / Berghuis, A.M.
CitationJournal: Biochim.Biophys.Acta / Year: 2006
Title: Crystal structure of CTP:glycerol-3-phosphate cytidylyltransferase from Staphylococcus aureus: examination of structural basis for kinetic mechanism.
Authors: Fong, D.H. / Yim, V.C.-N. / D'Elia, M.A. / Brown, E.D. / Berghuis, A.M.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycerol-3-phosphate cytidylyltransferase
B: glycerol-3-phosphate cytidylyltransferase
C: glycerol-3-phosphate cytidylyltransferase
D: glycerol-3-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)63,3734
Polymers63,3734
Non-polymers00
Water00
1
A: glycerol-3-phosphate cytidylyltransferase
B: glycerol-3-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)31,6862
Polymers31,6862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-9 kcal/mol
Surface area11990 Å2
MethodPISA
2
C: glycerol-3-phosphate cytidylyltransferase
D: glycerol-3-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)31,6862
Polymers31,6862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.150, 92.150, 156.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
glycerol-3-phosphate cytidylyltransferase / GCT / CDP-GLYCEROL PYROPHOSPHORYLASE / TEICHOIC ACID BIOSYNTHESIS PROTEIN D


Mass: 15843.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pKK223 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110
References: UniProt: O05155, glycerol-3-phosphate cytidylyltransferase

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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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% ethylene glycol, 3% D(+) glucose, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2000 / Details: mirror
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 15217 / Num. obs: 15217 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 7
Reflection shellResolution: 3→3.11 Å / % possible all: 70.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1COZ

1coz


Resolution: 3→46.08 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 179059.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1483 10.1 %RANDOM
Rwork0.239 ---
obs0.239 14712 92.4 %-
all-15926 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4364 Å2 / ksol: 0.404294 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.89 Å213.16 Å20 Å2
2--7.89 Å20 Å2
3----15.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 0 0 3880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.672.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 185 10.6 %
Rwork0.329 1565 -
obs-1565 66.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ctp.parctp.top

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