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- PDB-2hur: Escherichia coli nucleoside diphosphate kinase -

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Basic information

Entry
Database: PDB / ID: 2hur
TitleEscherichia coli nucleoside diphosphate kinase
ComponentsNUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / TYPE II TETRAMER
Function / homology
Function and homology information


purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMoynie, L. / Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
Citation
Journal: Proteins / Year: 2007
Title: The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family
Authors: Moynie, L. / Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
#1: Journal: J.Bacteriol. / Year: 1995
Title: Nucleoside diphosphate kinase from Escherichia coli
Authors: Almaula, N. / Lu, Q. / Delgado, J. / Belkin, S. / Inouye, M.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 A resolution
Authors: Williams, R.L. / Oren, D.A. / Inouye, S. / Inouye, M. / Arnold, E.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8 A resolution.
Authors: LeBras, G. / Lascu, I. / Lacombe, M.L. / Janin, J.
History
DepositionJul 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,67812
Polymers92,1016
Non-polymers5766
Water12,917717
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7858
Polymers61,4014
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7858
Polymers61,4014
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
3
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8934
Polymers30,7002
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-92 kcal/mol
Surface area23520 Å2
MethodPQS
4
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8934
Polymers30,7002
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-91 kcal/mol
Surface area22460 Å2
MethodPQS
5
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8934
Polymers30,7002
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)118.904, 76.095, 104.588
Angle α, β, γ (deg.)90.00, 112.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-261-

HOH

21B-296-

HOH

31B-297-

HOH

41C-219-

HOH

51E-303-

HOH

61F-280-

HOH

71F-323-

HOH

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Components

#1: Protein
NUCLEOSIDE DIPHOSPHATE KINASE / Nucleoside-diphosphate kinase / E.C.2.7.4.6 / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 15350.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ndk / Plasmid: PJC20 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A763, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M AMMONIUM SULPHATE, 25% PEG 4000 0.1 M SODIUM ACETATE/ACETIC ACID, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.62→38.05 Å / Num. all: 108681 / Num. obs: 108681 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.09 / Net I/σ(I): 16.6
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.38 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB FILE 2NCK

2nck


Resolution: 1.62→38.05 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2343463.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 5451 5 %RANDOM
Rwork0.191 ---
all0.196 108681 --
obs0.191 108681 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0217 Å2 / ksol: 0.368627 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å23.96 Å2
2--1.33 Å20 Å2
3----0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.62→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 30 717 7239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 894 5 %
Rwork0.263 16974 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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