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- PDB-7ckj: Crystal structure of CMP kinase in complex with CMP from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 7ckj
TitleCrystal structure of CMP kinase in complex with CMP from Thermus thermophilus HB8
ComponentsCytidylate kinase
KeywordsTRANSFERASE / CMP kinase / CMP complex / open conformation / nucleotide metabolism / Structural Genomics / PSI-2 / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


(d)CMP kinase / CMP kinase activity / dCMP kinase activity / pyrimidine nucleotide metabolic process / ATP binding / cytoplasm
Similarity search - Function
Cytidylate kinase / Cytidylate kinase domain / Cytidylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Cytidylate kinase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17770089 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)20570131 Japan
CitationJournal: PLoS ONE / Year: 2020
Title: The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor.
Authors: Mega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJul 17, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 29, 2020ID: 3AKE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9082
Polymers22,5851
Non-polymers3231
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-4 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.746, 61.746, 111.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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 HB8 (bacteria) / Strain: HB8 / Gene: cmk, TTHA0458 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL35, (d)CMP kinase
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M BIS-TRIS, 3.5M Sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2006
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38410 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.066 / Χ2: 1.997 / Net I/σ(I): 28 / Num. measured all: 312320
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.5-1.557.80.34338012.04199.8
1.55-1.628.10.24938351.933199.9
1.62-1.698.10.1938181.867199.9
1.69-1.788.20.13938251.7341100
1.78-1.898.20.09238371.671100
1.89-2.048.20.06638361.6531100
2.04-2.248.30.05338611.6891100
2.24-2.568.30.04938541.8711100
2.56-3.238.30.05338372.274199.9
3.23-507.90.06339063.275199.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
ARP/wARP7.1model building
CNSrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CMK
Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 3834 10 %RANDOM
Rwork0.2058 34495 --
obs-38329 99.9 %-
Solvent computationBsol: 45.9207 Å2
Displacement parametersBiso max: 53.42 Å2 / Biso mean: 19.4958 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å20 Å2
2--3.07 Å20 Å2
3----6.139 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 21 135 1733
Biso mean--16.4 27.71 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3271.5
X-RAY DIFFRACTIONc_scbond_it1.9082
X-RAY DIFFRACTIONc_mcangle_it1.9942
X-RAY DIFFRACTIONc_scangle_it2.8062.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.001
RfactorNum. reflection% reflection
Rfree0.252 667 10.5 %
Rwork0.231 5677 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6c5p.param

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