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- PDB-1be4: NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA -

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Basic information

Entry
Database: PDB / ID: 1be4
TitleNUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA
ComponentsNUCLEOSIDE DIPHOSPHATE TRANSFERASE
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / Ribavirin ADME / Azathioprine ADME / DNA nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ribosomal small subunit binding ...Interconversion of nucleotide di- and triphosphates / Ribavirin ADME / Azathioprine ADME / DNA nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ribosomal small subunit binding / 3'-5' exonuclease activity / lactation / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / cell differentiation / early endosome / GTP binding / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytosol
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
CYCLIC GUANOSINE MONOPHOSPHATE / Nucleoside diphosphate kinase A 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLadner, J.E. / Abdulaev, N.G. / Kakuev, D.L. / Karaschuk, G.N. / Tordova, M. / Eisenstein, E. / Fujiwara, J.H. / Ridge, K.D. / Gilliland, G.L.
CitationJournal: Biochemistry / Year: 1998
Title: Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure.
Authors: Abdulaev, N.G. / Karaschuk, G.N. / Ladner, J.E. / Kakuev, D.L. / Yakhyaev, A.V. / Tordova, M. / Gaidarov, I.O. / Popov, V.I. / Fujiwara, J.H. / Chinchilla, D. / Eisenstein, E. / Gilliland, G.L. / Ridge, K.D.
History
DepositionMay 19, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: 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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
B: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
C: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6086
Polymers51,5733
Non-polymers1,0363
Water5,008278
1
A: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
B: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
C: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
hetero molecules

A: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
B: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
C: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,21612
Polymers103,1456
Non-polymers2,0716
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area20330 Å2
ΔGint-105 kcal/mol
Surface area32780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.610, 128.610, 88.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE TRANSFERASE


Mass: 17190.844 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: RETINA / Organ: EYE / Production host: Escherichia coli (E. coli) / References: UniProt: P52175, nucleoside-diphosphate kinase
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 3.5 Å3/Da / Density % sol: 65.19 %
Crystal growpH: 7 / Details: pH 7
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drops were formed by combining equal volumes of protein solution and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mMcGMP1drop
2100 mmTris-HCl1reservoir
32.3 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 30274 / % possible obs: 89 % / Redundancy: 4.6 % / Rsym value: 0.109 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.51 Å / Mean I/σ(I) obs: 1.3 / % possible all: 60
Reflection
*PLUS
Rmerge(I) obs: 0.109
Reflection shell
*PLUS
% possible obs: 60 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NSK

1nsk


Resolution: 2.4→20 Å / Isotropic thermal model: TNT BCORREL
Details: X-PLOR SIMULATED ANNEALING, SLOW COOLING, POSITIONAL AND B-FACTOR REFINEMENT WAS USED WITH 10% OF THE DATA RESERVED FOR R-FREE. R-FREE WENT FROM 0.398 - 0.366 WHILE THE WORKING R WENT TO 0. ...Details: X-PLOR SIMULATED ANNEALING, SLOW COOLING, POSITIONAL AND B-FACTOR REFINEMENT WAS USED WITH 10% OF THE DATA RESERVED FOR R-FREE. R-FREE WENT FROM 0.398 - 0.366 WHILE THE WORKING R WENT TO 0.259. THEN TNT WAS USED FOR THE FINAL REFINEMENT WITHOUT R-FREE.
RfactorNum. reflection% reflection
all0.198 26318 -
obs-26318 89 %
Solvent computationBsol: 283.9 Å2 / ksol: 0.809 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 69 278 3968
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02437771.5
X-RAY DIFFRACTIONt_angle_deg5.5350701.3
X-RAY DIFFRACTIONt_dihedral_angle_d19.86222560
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.024931.8
X-RAY DIFFRACTIONt_gen_planes0.0265375.8
X-RAY DIFFRACTIONt_it11.27436991
X-RAY DIFFRACTIONt_nbd0.06216210
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.026 / Weight: 5.8

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