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- PDB-2hve: S120G mutant of human nucleoside diphosphate kinase A complexed w... -

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Basic information

Entry
Database: PDB / ID: 2hve
TitleS120G mutant of human nucleoside diphosphate kinase A complexed with ADP
ComponentsNucleoside diphosphate kinase A
KeywordsSIGNALING PROTEIN / TRANSFERASE / S120G MUTANT / COMPLEX ADP
Function / homology
Function and homology information


DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process ...DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / early endosome / negative regulation of cell population proliferation / GTP binding / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / 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 (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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 A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsGiraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
Citation
Journal: J.Bioenerg.Biomembr. / Year: 2006
Title: Crystal Structures of S120G Mutant and Wild Type of Human Nucleoside Diphosphate Kinase A in Complex with ADP
Authors: Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
#1: Journal: Proteins / Year: 2002
Title: Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor
Authors: Min, K. / Song, H.K. / Chang, C. / Kim, S.Y. / Lee, K.J. / Suh, S.W.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases
Authors: Chen, Y. / Gallois-Montbrun, S. / Schneider, B. / Deville-Bonne, D. / Janin, J.
History
DepositionJul 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7046
Polymers51,4223
Non-polymers1,2823
Water2,720151
1
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)105,40712
Polymers102,8446
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area21180 Å2
ΔGint-125 kcal/mol
Surface area33250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.824, 114.824, 89.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-161-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase A / E.C.2.7.4.6 / NDK A / NDP kinase A / Tumor metastatic process-associated protein / Metastasis inhibition factor ...NDK A / NDP kinase A / Tumor metastatic process-associated protein / Metastasis inhibition factor nm23 / nm23-H1 / Granzyme A-activated DNase / GAAD


Mass: 17140.693 Da / Num. of mol.: 3 / Mutation: S120G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME1, NDPKA, NM23 / Plasmid: PET-21 / Production host: Escherichia coli (E. coli) / References: UniProt: P15531, nucleoside-diphosphate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4 M AMMONIUM SULPHATE, 10 MM ADP, 20 MM MGCL2, 4 MM DTT, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.402→40 Å / Num. all: 22088 / Num. obs: 22088 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 49.109 Å2 / Rsym value: 0.1 / Net I/σ(I): 21.4
Reflection shellResolution: 2.402→2.53 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 4 / Rsym value: 0.4 / % possible all: 86.7

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Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.2refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UCN

1ucn


Resolution: 2.402→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.227 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27725 1192 5.1 %RANDOM
Rwork0.21784 ---
all0.22078 22088 --
obs0.22078 22088 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.111 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.402→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 81 151 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223757
X-RAY DIFFRACTIONr_bond_other_d0.0020.023369
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9795085
X-RAY DIFFRACTIONr_angle_other_deg2.31537839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71423.966174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15115642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9841524
X-RAY DIFFRACTIONr_chiral_restr0.0680.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024137
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02783
X-RAY DIFFRACTIONr_nbd_refined0.1970.2758
X-RAY DIFFRACTIONr_nbd_other0.2070.23451
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21782
X-RAY DIFFRACTIONr_nbtor_other0.0870.21847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4410.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.25
X-RAY DIFFRACTIONr_mcbond_it1.0271.52943
X-RAY DIFFRACTIONr_mcbond_other0.0251.5942
X-RAY DIFFRACTIONr_mcangle_it0.9423594
X-RAY DIFFRACTIONr_scbond_it1.4831814
X-RAY DIFFRACTIONr_scangle_it1.8784.51491
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 81 -
Rwork0.337 1407 -
obs--86.11 %

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