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- PDB-2dy9: Crystal structure of nucleoside diphosphate kinase in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 2dy9
TitleCrystal structure of nucleoside diphosphate kinase in complex with ADP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / nucleoside binding / kinase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of nucleoside diphosphate kinase in complex with ADP
Authors: Kato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionSep 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_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: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2788
Polymers36,6852
Non-polymers5936
Water3,981221
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,83424
Polymers110,0546
Non-polymers1,78018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area23970 Å2
ΔGint-295 kcal/mol
Surface area34240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.835, 69.835, 106.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 18342.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: ndk / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58429, nucleoside-diphosphate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na Citrate, Bicine, 1mM ADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 26, 2005
RadiationMonochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→34.92 Å / Num. obs: 19689 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.078 / Net I/σ(I): 32.1
Reflection shellResolution: 2.01→2.08 Å / Rsym value: 0.298 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CWK

2cwk


Resolution: 2.01→34.92 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1475359.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: This is a twinned structure. The twinning operator is (h,k,l) -> (h,-h-k,-l) and the twinning fraction is 0.404.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 918 4.7 %RANDOM
Rwork0.122 ---
obs-19663 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0422 Å2 / ksol: 0.390506 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.289 Å2-0.391 Å20 Å2
2--0.289 Å20 Å2
3----0.577 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.01→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 32 221 2746
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 2.01→2.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.215 106 4.3 %
Rwork0.164 2342 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2adp.paramadp.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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