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- PDB-3akd: Crystal structure of CMP kinase in complex with CDP from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 3akd
TitleCrystal structure of CMP kinase in complex with CDP from Thermus thermophilus HB8
ComponentsCytidylate kinase
KeywordsTRANSFERASE / CMP kinase / CDP complex / open conformation / nucleotide metabolism
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'-DIPHOSPHATE / Cytidylate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
CitationJournal: To be Published
Title: The crystal structure of the tertiary complex of CMP kinase with a phosphoryl group acceptor and a donor from Thermus thermophilus HB8
Authors: Mega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJul 12, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9882
Polymers22,5851
Non-polymers4031
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.929, 61.929, 111.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 (bacteria) / Strain: HB8 / Gene: TTHA0458 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL35, UMP/CMP kinase
#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M BIS-TRIS propane, 3.5M sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 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: 1.6→50 Å / Num. obs: 29707 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 53
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1768 / % possible all: 55.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
ARP/wARP7.1model building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CMK

2cmk


Resolution: 1.6→38.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1453360.21 / 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
Rfree0.236 2961 10 %RANDOM
Rwork0.21 ---
obs0.21 26704 93.1 %-
all-29665 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9677 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.11 Å20 Å20 Å2
2--5.11 Å20 Å2
3----10.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 25 103 1668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d3.62
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.305 371 10.4 %
Rwork0.255 3184 -
obs-3184 67.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2CDP.paramCDP.top
X-RAY DIFFRACTION4water.paramwater.top

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