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- PDB-2h92: Crystal Structure of Staphylococcus aureus Cytidine Monophosphate... -

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Basic information

Entry
Database: PDB / ID: 2h92
TitleCrystal Structure of Staphylococcus aureus Cytidine Monophosphate Kinase in complex with cytidine-5'-monophosphate
ComponentsCytidylate kinase
KeywordsTRANSFERASE / Rossmann fold
Function / homology
Function and homology information


(d)CMP kinase / cytidylate kinase activity / pyrimidine nucleotide metabolic process / ATP binding / cytoplasm
Similarity search - Function
Cytidylate kinase / Cytidylate kinase domain / Cytidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Cytidylate kinase / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDhaliwal, B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate.
Authors: Dhaliwal, B. / Ren, J. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K.
History
DepositionJun 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / 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

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Assembly

Deposited unit
A: Cytidylate kinase
B: Cytidylate kinase
C: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,33910
Polymers73,8873
Non-polymers1,4527
Water6,017334
1
A: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0483
Polymers24,6291
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2424
Polymers24,6291
Non-polymers6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0483
Polymers24,6291
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.890, 157.890, 76.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Cytidylate kinase / / Cytidine monophosphate kinase


Mass: 24628.996 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cmk / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: Q1YBX2, UniProt: P63807*PLUS, UMP/CMP kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 1.6M ammonium sulfate, 0.1M Hepes, 2% PEG 200, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 48287 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 %
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.9 % / % possible all: 100

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Processing

Software
NameClassification
ADSCdata collection
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KDO

1kdo


Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 2420 RANDOM
Rwork0.211 --
all0.211 48270 -
obs0.214 48267 -
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 90 334 5512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0083
X-RAY DIFFRACTIONc_angle_deg1.27
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4c.par
X-RAY DIFFRACTION5peg2.par

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