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- PDB-1wkl: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus t... -

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Basic information

Entry
Database: PDB / ID: 1wkl
TitleCrystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with ATP and ADP
Componentsnucleotide diphosphate kinase
KeywordsTRANSFERASE / nucleotide diphosphate kinase / complex with ATP and ADP / reaction intermediate / Thermus thermophilus HB8 / kinase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / 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 / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHONIC ACID / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTakeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8
Authors: Takeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S.
History
DepositionJun 1, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 23, 2014Group: Experimental preparation
Revision 1.4Oct 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.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_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.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.ptnr1_label_seq_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: nucleotide diphosphate kinase
B: nucleotide diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7746
Polymers30,7342
Non-polymers1,0414
Water1,60389
1
A: nucleotide diphosphate kinase
B: nucleotide diphosphate kinase
hetero molecules

A: nucleotide diphosphate kinase
B: nucleotide diphosphate kinase
hetero molecules

A: nucleotide diphosphate kinase
B: nucleotide diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,32318
Polymers92,2016
Non-polymers3,12212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15890 Å2
ΔGint-131 kcal/mol
Surface area32290 Å2
MethodPISA, PQS
2
A: nucleotide diphosphate kinase
B: nucleotide diphosphate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)190,64736
Polymers184,40312
Non-polymers6,24424
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
crystal symmetry operation11_556-x+y,y,-z+3/21
crystal symmetry operation12_566x,x-y+1,-z+3/21
Buried area35900 Å2
ΔGint-279 kcal/mol
Surface area60460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.897, 122.897, 105.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y+1, x-y+1, z and -x+y, -x+1, z.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein nucleotide diphosphate kinase


Mass: 15366.903 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ndk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLV5, nucleoside-diphosphate kinase

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Non-polymers , 5 types, 93 molecules

#2: Chemical ChemComp-PHS / PHOSPHONIC ACID


Mass: 81.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O3P
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 14% PEG4000, 0.09M Ammonium Acetate, 18% glycerol, 0.1M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 497844 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 20.3 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 72.6
Reflection shellResolution: 2.2→2.8 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 20 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WKJ

1wkj


Resolution: 2.2→50 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2326 -RANDOM
Rwork0.217 ---
all-24463 --
obs-23548 96.5 %-
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.259 Å21.325 Å20 Å2
2---2.259 Å20 Å2
3---4.518 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 63 89 2310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3

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