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- PDB-1dek: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP -

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Basic information

Entry
Database: PDB / ID: 1dek
TitleDEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP
ComponentsDEOXYNUCLEOSIDE MONOPHOSPHATE KINASE
KeywordsPHOSPHOTRANSFERASE / TRANSFERASE
Function / homology
Function and homology information


deoxynucleoside phosphate kinase activity, ATP as phosphate donor / dGMP kinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / dTMP kinase activity / ATP binding
Similarity search - Function
Recoverin; domain 1 - #70 / Deoxynucleotide monophosphate kinase, N-terminal / : / Deoxynucleotide monophosphate kinase / Recoverin; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Recoverin; domain 1 - #70 / Deoxynucleotide monophosphate kinase, N-terminal / : / Deoxynucleotide monophosphate kinase / Recoverin; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxynucleotide monophosphate kinase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsTeplyakov, A. / Sebastiao, P.
Citation
Journal: EMBO J. / Year: 1996
Title: Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
Authors: Teplyakov, A. / Sebastiao, P. / Obmolova, G. / Perrakis, A. / Brush, G.S. / Bessman, M.J. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of Bacteriophage T4 Deoxynucleotide Kinase
Authors: Sebastiao, P. / Obmolova, G. / Brush, G.S. / Bessman, M.J. / Teplyakov, A.
History
DepositionJan 9, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details / _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: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE
B: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5576
Polymers54,8142
Non-polymers7434
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-31 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.200, 58.500, 75.700
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98924, -0.12704, 0.0726), (-0.12192, 0.44125, -0.88906), (0.08091, -0.88835, -0.45199)
Vector: 131.01459, 28.26046, 26.00653)

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Components

#1: Protein DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE


Mass: 27407.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 1 / Plasmid: PBK5 / Gene (production host): 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04531, EC: 2.7.4.13
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 59 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMTris-HCl1drop
37 mMDTT1drop
45 mMdGMP1drop
511-14 %(v/v)PEG40001reservoir
6200 mMmagnesium acetate1reservoir
77 mMDTT1reservoir
82 %dioxane1reservoir
9100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 30, 1994 / Details: ELLIPTICAL MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 42100 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 99 % / Num. measured all: 202204

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
RefinementResolution: 2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.187 --
obs-41793 99 %
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 48 287 4107
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0280.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.14
X-RAY DIFFRACTIONp_mcangle_it6.27
X-RAY DIFFRACTIONp_scbond_it7.68
X-RAY DIFFRACTIONp_scangle_it10.79
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1480.15
X-RAY DIFFRACTIONp_singtor_nbd0.1290.3
X-RAY DIFFRACTIONp_multtor_nbd0.1980.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.53
X-RAY DIFFRACTIONp_staggered_tor18.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 3 / Rfactor all: 0.187 / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS

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