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- PDB-2a2z: Crystal Structure of human deoxycytidine kinase in complex with d... -

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Basic information

Entry
Database: PDB / ID: 2a2z
TitleCrystal Structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / Nucleoside Kinase / uridine diphosphate
Function / homology
Function and homology information


deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / Deoxynucleoside kinase domain / Deoxynucleoside 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
2'-DEOXYCYTIDINE / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsGodsey, M.H. / Ort, S. / Sabini, E. / Konrad, M. / Lavie, A.
CitationJournal: Biochemistry / Year: 2006
Title: Structural basis for the preference of UTP over ATP in human deoxycytidine kinase: illuminating the role of main-chain reorganization.
Authors: Godsey, M.H. / Ort, S. / Sabini, E. / Konrad, M. / Lavie, A.
History
DepositionJun 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN UDP 301, MO3 302, DCZ 304 are assoicated with protein chain A UDP 401, MO3 402, DCZ 404 ...HETEROGEN UDP 301, MO3 302, DCZ 304 are assoicated with protein chain A UDP 401, MO3 402, DCZ 404 are assoicated with protein chain B UDP 501, MO3 502, DCZ 504 are assoicated with protein chain C UDP 601, MO3 602, DCZ 604 are assoicated with protein chain D

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidine kinase
B: Deoxycytidine kinase
C: Deoxycytidine kinase
D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,25918
Polymers116,5564
Non-polymers2,70314
Water1,20767
1
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6299
Polymers58,2782
Non-polymers1,3517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-42 kcal/mol
Surface area18260 Å2
MethodPISA
2
C: Deoxycytidine kinase
D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6299
Polymers58,2782
Non-polymers1,3517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-46 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.180, 110.850, 155.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe Biological assembly is a dimer. There are two dimers per ASU.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Deoxycytidine kinase / / dCK


Mass: 29139.004 Da / Num. of mol.: 4 / Mutation: residues 65-79 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BLD21DE3 / References: UniProt: P27707, deoxycytidine kinase

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Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-DCZ / 2'-DEOXYCYTIDINE / Deoxycytidine


Type: DNA OH 5 prime terminus / Mass: 227.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N3O4
#5: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.4 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 1000, MPD, Calcium Chloride, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97626 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2004 / Details: Mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.02→30 Å / Num. all: 22334 / Num. obs: 22297 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.125 / Rsym value: 0.118 / Net I/σ(I): 12.63
Reflection shellResolution: 3.02→3.1 Å / % possible obs: 91.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.48 / Num. measured obs: 17495 / Num. unique all: 3257 / Num. unique obs: 3257 / Rsym value: 0.41 / % possible all: 91.2

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Phasing

Phasing MRRfactor: 0.491 / Cor.coef. Fo:Fc: 0.641
Highest resolutionLowest resolution
Rotation3 Å28.66 Å
Translation3 Å28.66 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 22202
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.74-10037.90.674501
8.57-10.7440.10.739511
7.5-8.5746.50.692503
6.82-7.548.40.688502
6.29-6.82520.71542
5.88-6.29500.707576
5.53-5.88460.728618
5.24-5.5337.70.781654
4.99-5.2434.90.801671
4.77-4.9938.70.795707
4.58-4.7733.80.804727
4.41-4.5835.60.819779
4.26-4.4135.20.832776
4.12-4.26370.818817
4-4.1236.40.821830
3.88-436.40.812882
3.78-3.8838.70.795887
3.68-3.78360.809928
3.59-3.6837.20.828920
3.51-3.5938.10.835982
3.43-3.5136.90.819959
3.36-3.4341.30.801993
3.29-3.3643.50.8051037
3.23-3.2941.10.7891047
3.16-3.2342.70.7951052
3.11-3.16490.7521077
3.02-3.1149.50.721724

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
DM4.2phasing
CNS1.1refinement
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1P60

1p60


Resolution: 3.02→29.66 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 2244 10.1 %RANDOM
Rwork0.246 ---
all0.25 22426 --
obs0.25 22202 99 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 22.1675 Å2 / ksol: 0.282504 e/Å3
Displacement parametersBiso max: 85.72 Å2 / Biso mean: 44.64 Å2 / Biso min: 0.79 Å2
Baniso -1Baniso -2Baniso -3
1--13.77 Å20 Å20 Å2
2--5.9 Å20 Å2
3---7.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.61 Å
Luzzati d res high-3.02
Refinement stepCycle: LAST / Resolution: 3.02→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7169 0 182 55 7406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.02-3.160.39626910.10.37223940.0242756266396.6
3.16-3.320.35427910.20.31724630.0212753274299.6
3.32-3.530.35828710.30.28525030.0212792279099.9
3.53-3.80.342639.60.26924860.0212763274999.5
3.8-4.190.29828110.20.22424680.0182766274999.3
4.19-4.790.24728310.20.19225010.0152810278499.1
4.79-6.030.273282100.22225310.0162833281399.3
6.03-29.660.26230010.30.21926130.0152969291398.1

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