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- PDB-1coz: CTP:GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE FROM BACILLUS SUBTILIS -

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Open data


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Basic information

Entry
Database: PDB / ID: 1coz
TitleCTP:GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE FROM BACILLUS SUBTILIS
ComponentsPROTEIN (GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE)
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycerol-3-phosphate cytidylyltransferase / glycerol-3-phosphate cytidylyltransferase activity / teichoic acid biosynthetic process / cell wall organization / 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
CYTIDINE-5'-TRIPHOSPHATE / Glycerol-3-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsWeber, C.H. / Park, Y.S. / Sanker, S. / Kent, C. / Ludwig, M.L.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
Authors: Weber, C.H. / Park, Y.S. / Sanker, S. / Kent, C. / Ludwig, M.L.
History
DepositionMay 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE)
B: PROTEIN (GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5574
Polymers30,5912
Non-polymers9662
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-24 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.500, 61.400, 56.400
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.9844, 0.1749, 0.0366), (0.1722, 0.8788, 0.4454), (0.0459, 0.4452, -0.8943)
Vector: -85.4015, -1.3742, 38.7824)

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Components

#1: Protein PROTEIN (GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE)


Mass: 15295.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: BR151-ESC168 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli)
References: UniProt: P27623, glycerol-3-phosphate cytidylyltransferase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.3 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.5
Details: 100 MM TRIS PH 8.5 200 MM LITHIUM SULFATE 30% PEG 3350 (BAKER)
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.3 mg/mlprotein1drop
255 mMTris1drop
30.63 mMEDTA1drop
40.63 mMdithiothreitol1drop
511 %PEG33501drop
675 mMlithium sulfate1drop
730 %PEG33501reservoir
8200 mMlithium sulfate1reservoir
9100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 16917 / % possible obs: 88.6 % / Redundancy: 2.68 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.061
Reflection shellResolution: 2→2.12 Å / Rsym value: 0.125 / % possible all: 66.4
Reflection
*PLUS
Num. measured all: 45342 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 83.8 % / Rmerge(I) obs: 0.125

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0
Details: BULK SOLVENT MODEL USED GROUP 1 FOR NCS RESTRAINTS: 1 - 37 AND 501 - 537, 47 - 73 AND 547 - 573, 76 - 81 AND 576 - 581, 88 - 93 AND 588 - 593, AND 108 - 126 AND 608 - 626. THE REMAINDER OF ...Details: BULK SOLVENT MODEL USED GROUP 1 FOR NCS RESTRAINTS: 1 - 37 AND 501 - 537, 47 - 73 AND 547 - 573, 76 - 81 AND 576 - 581, 88 - 93 AND 588 - 593, AND 108 - 126 AND 608 - 626. THE REMAINDER OF THE PROTEIN ATOMS WERE IN GROUP 2. THIS P 21 CRYSTAL DISPLAYS MEROHEDRAL TWINNING AND CAN BE INDEXED AS ORTHORHOMBIC C 2 2 21
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1576 10 %RANDOM
Rwork0.196 ---
obs0.196 15720 84.1 %-
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-8 Å
Luzzati sigma a0.2 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 58 106 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it31.5
X-RAY DIFFRACTIONx_mcangle_it4.322
X-RAY DIFFRACTIONx_scbond_it5.562
X-RAY DIFFRACTIONx_scangle_it8.42.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11YESX-RAY DIFFRACTION1.1300
22X-RAY DIFFRACTION1.8420
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 216 10.5 %
Rwork0.271 1844 -
obs--66.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2CTP.PARCTP.TOP
X-RAY DIFFRACTION3WAT.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.271

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