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- PDB-3w90: Crystal structure of CMP kinase from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 3w90
TitleCrystal structure of CMP kinase from Thermus thermophilus HB8
ComponentsCytidylate kinase
KeywordsTRANSFERASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / kinase / CMP
Function / homology
Function and homology information


(d)CMP kinase / CMP kinase activity / dCMP kinase activity / pyrimidine nucleotide metabolic process / phosphorylation / 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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNakagawa, N. / Mega, R. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of CMP kinase: insights into initial substrate recognition and reaction mechanisms
Authors: Mega, R. / Nakagawa, N. / Masui, R. / Kuramitsu, S.
History
DepositionMar 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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: Cytidylate kinase


Theoretical massNumber of molelcules
Total (without water)22,5851
Polymers22,5851
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.727, 48.382, 110.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytidylate kinase / / CK / Cytidine monophosphate kinase / CMP kinase


Mass: 22584.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0458 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL35, (d)CMP kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.11 Å3/Da / Density % sol: 41.58 % / Mosaicity: 0.204 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 60mM sodium acetate, 40% ethylene glycol, 15% PEG1000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.9794 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 3, 2003
RadiationMonochromator: transparent double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 26020 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.062 / Χ2: 2.471 / Net I/σ(I): 28.4
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.660.27725491.697199.6
1.66-1.720.23525671.8351100
1.72-1.80.19125442.0631100
1.8-1.90.14325722.4041100
1.9-2.020.11125702.7191100
2.02-2.170.09325582.9631100
2.17-2.390.08126163.021100
2.39-2.740.07326182.9551100
2.74-3.450.05726402.3861100
3.45-500.04527862.338199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.3refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W8N

3w8n


Resolution: 1.65→44.29 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8527 / Data cutoff high absF: 868369 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2308 9.9 %RANDOM
Rwork0.214 ---
obs-23431 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.8824 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 64.77 Å2 / Biso mean: 21.4725 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---0.52 Å20 Å2
3----1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.65→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 0 170 1676
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.84
X-RAY DIFFRACTIONc_mcbond_it2.031.5
X-RAY DIFFRACTIONc_mcangle_it2.92
X-RAY DIFFRACTIONc_scbond_it3.122
X-RAY DIFFRACTIONc_scangle_it4.372.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 367 9.8 %
Rwork0.234 3383 -
all-3750 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2dna-rna.paramdna-rna.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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