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- PDB-3bbc: Crystal structure of R88A mutant of the NM23-H2 transcription factor -

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Basic information

Entry
Database: PDB / ID: 3bbc
TitleCrystal structure of R88A mutant of the NM23-H2 transcription factor
ComponentsNucleoside diphosphate kinase B
KeywordsTRANSFERASE / transcriptional factor / kinase / NM23 gen / hexamer / cancer / Activator / Anti-oncogene / ATP-binding / Cell cycle / DNA-binding / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Nucleus / Phosphorylation / Transcription regulation
Function / homology
Function and homology information


regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process ...regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / GTP biosynthetic process / histidine kinase / ruffle / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / cell periphery / GDP binding / lamellipodium / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / transcription coactivator activity / cell adhesion / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / nucleus / 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
Nucleoside diphosphate kinase B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWeichsel, A. / Montfort, W.R.
Citation
Journal: Mol.Cancer Ther. / Year: 2009
Title: NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1.
Authors: Dexheimer, T.S. / Carey, S.S. / Zuohe, S. / Gokhale, V.M. / Hu, X. / Murata, L.B. / Maes, E.M. / Weichsel, A. / Sun, D. / Meuillet, E.J. / Montfort, W.R. / Hurley, L.H.
#1: Journal: Structure / Year: 1995
Title: X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.
Authors: Morera, S. / Lacombe, M.L. / Xu, Y. / LeBras, G. / Janin, J.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase B
B: Nucleoside diphosphate kinase B
C: Nucleoside diphosphate kinase B
D: Nucleoside diphosphate kinase B
E: Nucleoside diphosphate kinase B
F: Nucleoside diphosphate kinase B


Theoretical massNumber of molelcules
Total (without water)102,6406
Polymers102,6406
Non-polymers00
Water19,5821087
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.756, 104.616, 118.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoside diphosphate kinase B / NDK B / NDP kinase B / nm23-H2 / C-myc purine-binding transcription factor PUF


Mass: 17106.744 Da / Num. of mol.: 6 / Mutation: R88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME2, NM23B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P22392, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1087 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 1500, 50 mM sodium citrate, 20 mM MgCl2, 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2003 / Details: bent Si-mirror
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→26.5 Å / Num. all: 98113 / Num. obs: 98113 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.4 / Num. unique all: 9666 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDISPLAYFdata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NUE

1nue


Resolution: 1.7→26.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.163 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21574 4899 5 %RANDOM
Rwork0.17376 ---
obs0.17589 93076 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.669 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.91 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 0 1087 8311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227564
X-RAY DIFFRACTIONr_bond_other_d0.0020.025338
X-RAY DIFFRACTIONr_angle_refined_deg1.721.95810221
X-RAY DIFFRACTIONr_angle_other_deg1.041312990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0595936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79323.732343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.375151375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5061550
X-RAY DIFFRACTIONr_chiral_restr0.1180.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021570
X-RAY DIFFRACTIONr_nbd_refined0.2190.21611
X-RAY DIFFRACTIONr_nbd_other0.2060.25935
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23742
X-RAY DIFFRACTIONr_nbtor_other0.0890.23882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2854
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.244
X-RAY DIFFRACTIONr_mcbond_it1.3031.55961
X-RAY DIFFRACTIONr_mcbond_other0.3071.51878
X-RAY DIFFRACTIONr_mcangle_it1.55127448
X-RAY DIFFRACTIONr_scbond_it2.70633478
X-RAY DIFFRACTIONr_scangle_it3.8494.52773
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 337 -
Rwork0.201 6778 -
obs-6778 99.04 %

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