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- PDB-2ocp: Crystal Structure of Human Deoxyguanosine Kinase -

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Basic information

Entry
Database: PDB / ID: 2ocp
TitleCrystal Structure of Human Deoxyguanosine Kinase
ComponentsDeoxyguanosine kinase
KeywordsTRANSFERASE / PROTEIN-NUCLEOTIDE COMPLEX
Function / homology
Function and homology information


dGTP metabolic process / purine deoxyribonucleoside metabolic process / guanosine metabolic process / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Purine salvage / mitochondrial ATP synthesis coupled electron transport ...dGTP metabolic process / purine deoxyribonucleoside metabolic process / guanosine metabolic process / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Purine salvage / mitochondrial ATP synthesis coupled electron transport / negative regulation of neuron projection development / mitochondrial matrix / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyguanosine kinase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJohansson, K. / Ramaswamy, S. / Ljungkrantz, C. / Knecht, W. / Piskur, J. / Munch-Petersen, B. / Eriksson, S. / Eklund, H.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structural Basis for Substrate Specificities of Cellular Deoxyribonucleoside Kinases.
Authors: Johansson, K. / Ramaswamy, S. / Ljungkrantz, C. / Knecht, W. / Piskur, J. / Munch-Petersen, B. / Eriksson, S. / Eklund, H.
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionJan 16, 2007ID: 1JAG
Revision 1.0Jan 16, 2007Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Deoxyguanosine kinase
B: Deoxyguanosine kinase
C: Deoxyguanosine kinase
D: Deoxyguanosine kinase
E: Deoxyguanosine kinase
F: Deoxyguanosine kinase
G: Deoxyguanosine kinase
H: Deoxyguanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,48416
Polymers226,5558
Non-polymers3,9298
Water3,603200
1
A: Deoxyguanosine kinase
B: Deoxyguanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6214
Polymers56,6392
Non-polymers9822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-19 kcal/mol
Surface area20330 Å2
MethodPISA
2
C: Deoxyguanosine kinase
D: Deoxyguanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6214
Polymers56,6392
Non-polymers9822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-19 kcal/mol
Surface area20310 Å2
MethodPISA
3
E: Deoxyguanosine kinase
F: Deoxyguanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6214
Polymers56,6392
Non-polymers9822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-19 kcal/mol
Surface area20300 Å2
MethodPISA
4
G: Deoxyguanosine kinase
H: Deoxyguanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6214
Polymers56,6392
Non-polymers9822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-19 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.180, 120.030, 154.350
Angle α, β, γ (deg.)90.00, 90.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Deoxyguanosine kinase / dGK


Mass: 28319.338 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DGUOK, DGK / Production host: Escherichia coli (E. coli) / References: UniProt: Q16854, deoxyguanosine kinase
#2: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, AMMONIUM ACETATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: May 11, 1999
RadiationMonochromator: DIAMOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 61311 / % possible obs: 97.5 % / Observed criterion σ(I): 2.2 / Redundancy: 3.5 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J90

1j90


Resolution: 2.8→30 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE STRUCTURE IS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY. ONLY MOLECULE A WAS BUILT INTO AVERAGE MAPS AND THE OTHER SEVEN (B-H) MOLECULES WERE GENERATED ACCORDING TO THE NCS ...Details: THE STRUCTURE IS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY. ONLY MOLECULE A WAS BUILT INTO AVERAGE MAPS AND THE OTHER SEVEN (B-H) MOLECULES WERE GENERATED ACCORDING TO THE NCS SYMMETRY AND ARE THUS IDENTICAL TO MOLECULE A.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3013 5 %RANDOM
Rwork0.265 ---
obs0.265 59741 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.88 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15392 0 240 200 15832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.812.5
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 488 5 %
Rwork0.379 9248 -
obs--95.8 %

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