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- PDB-3w8n: Open form structure of CMP kinase in complex with CMP from Thermu... -

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Basic information

Entry
Database: PDB / ID: 3w8n
TitleOpen form structure of CMP kinase in complex with CMP 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 / ATP binding / cytoplasm
Similarity search - Function
Cytidylate kinase / Cytidylate kinase domain / Cytidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Cytidylate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 19, 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 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0492
Polymers22,7261
Non-polymers3231
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.212, 49.212, 98.051
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 22725.502 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): B834(DE3) / References: UniProt: Q5SL35, (d)CMP kinase
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.22 % / Mosaicity: 0.354 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10mM CMP, 10mM MgCl2, 0.6M sodium succinate, pH 7.0, 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: 0.9791 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 10, 2004
RadiationMonochromator: transparent double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 20.39 / Number: 52425 / Rmerge(I) obs: 0.049 / Χ2: 1.77 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 26811 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.745099.410.0321.717
3.764.7499.810.0371.88
3.293.7699.610.0462.249
2.993.2999.510.0562.145
2.772.9999.510.0721.938
2.612.7799.610.0931.763
2.482.6199.510.1241.749
2.372.4899.310.1511.533
2.282.3799.410.2051.379
2.22.2899.210.2621.298
ReflectionResolution: 2.2→50 Å / Num. obs: 26811 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.049 / Χ2: 1.767 / Net I/σ(I): 23.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.280.26226841.298199.2
2.28-2.370.20526461.379199.4
2.37-2.480.15126921.533199.3
2.48-2.610.12426711.749199.5
2.61-2.770.09326961.763199.6
2.77-2.990.07226441.938199.5
2.99-3.290.05627252.145199.5
3.29-3.760.04626692.249199.6
3.76-4.740.03726821.88199.8
4.74-500.03227021.717199.4

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0 / Reflection: 12904 / Reflection acentric: 12904 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
6.3-39.0860.950.95562562
3.9-6.30.930.9317831783
3.1-3.90.860.8622412241
2.8-3.10.660.6622412241
2.4-2.80.380.3838303830
2.2-2.40.180.1822472247

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
CNS1.3refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→42.62 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8396 / Data cutoff high absF: 821362 / 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 2462 9.5 %RANDOM
Rwork0.199 ---
obs-26009 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7231 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 85 Å2 / Biso mean: 37.6258 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 21 84 1623
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it3.022
X-RAY DIFFRACTIONc_scbond_it3.812
X-RAY DIFFRACTIONc_scangle_it5.062.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 411 10.2 %
Rwork0.264 3632 -
all-4043 -
obs--89.6 %
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
X-RAY DIFFRACTION6c5p.paramc5p.top

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