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- PDB-1del: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP AND AMP -

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Basic information

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


(deoxy)nucleoside-phosphate kinase / (deoxy)nucleoside-phosphate kinase activity / phosphorylation / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxynucleotide monophosphate kinase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 1.3Feb 7, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_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: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE
B: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8087
Polymers54,7182
Non-polymers1,0905
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-36 kcal/mol
Surface area21560 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: (-0.98807, -0.13116, 0.08074), (-0.13091, 0.43905, -0.88887), (0.08114, -0.88883, -0.45099)
Vector: 130.82207, 28.7169, 25.97971)

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Components

#1: Protein DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE


Mass: 27359.111 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, (deoxy)nucleoside-phosphate kinase
#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 / Deoxyguanosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: X11 / Wavelength: 0.92
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 31836 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.065
Reflection
*PLUS
Num. measured all: 96619

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
RefinementResolution: 2.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.186 --
obs-31623 95.9 %
Displacement parametersBiso mean: 39.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 71 222 4061
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0260.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.14
X-RAY DIFFRACTIONp_mcangle_it6.37
X-RAY DIFFRACTIONp_scbond_it88
X-RAY DIFFRACTIONp_scangle_it11.29
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1470.15
X-RAY DIFFRACTIONp_singtor_nbd0.1340.3
X-RAY DIFFRACTIONp_multtor_nbd0.1930.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor1915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 3 / Rfactor all: 0.186 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.027

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