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- PDB-1bhn: NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA -

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Basic information

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


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / endocytosis / nervous system development / cell differentiation / ATP binding / metal ion binding ...nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / endocytosis / nervous system development / cell differentiation / ATP binding / metal ion binding / nucleus / plasma membrane / cytoplasm
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
GUANOSINE-3',5'-MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase A 1
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: Acta Crystallogr.,Sect.D / Year: 1999
Title: The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina.
Authors: Ladner, J.E. / Abdulaev, N.G. / Kakuev, D.L. / Tordova, M. / Ridge, K.D. / Gilliland, G.L.
History
DepositionJun 10, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
D: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
E: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
F: NUCLEOSIDE DIPHOSPHATE TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,44018
Polymers103,7106
Non-polymers4,73012
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25050 Å2
ΔGint-123 kcal/mol
Surface area31090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.880, 92.110, 131.630
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 TRANSFERASE


Mass: 17284.955 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: EYE / Organ: RETINA / Production host: Escherichia coli (E. coli) / References: UniProt: P52174, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-35G / GUANOSINE-3',5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.7 Å3/Da / Density % sol: 53.16 %
Crystal growpH: 5 / Details: pH 5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop contains equal volume of the reservoir solution
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-ID
1mg/mlprotein1drop
2mMGTP1drop
3mMcGMP1drop
4mMsodium acetate1reservoir
5mMammonium acetate1reservoir
6%(w/v)PEG40001reservoir

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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: Jan 15, 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: 41872 / % possible obs: 79 % / Redundancy: 4 % / Rsym value: 0.122 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.51 Å / Mean I/σ(I) obs: 1.4 / % possible all: 60
Reflection
*PLUS
Num. measured all: 165667 / Rmerge(I) obs: 0.122
Reflection shell
*PLUS
Lowest resolution: 2.54 Å / % possible obs: 60 % / Rmerge(I) obs: 0.384

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED STRUCTURE OF THE B ISOFORM

Resolution: 2.4→20 Å / Isotropic thermal model: TNT BCORREL
RfactorNum. reflection% reflection
all0.2 34202 -
obs-34202 79 %
Solvent computationBsol: 231.6 Å2 / ksol: 0.672 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 306 306 7848
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02177341.4
X-RAY DIFFRACTIONt_angle_deg5.132103981.3
X-RAY DIFFRACTIONt_dihedral_angle_d20.4645480
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0221861.6
X-RAY DIFFRACTIONt_gen_planes0.02610805
X-RAY DIFFRACTIONt_it8.4973981
X-RAY DIFFRACTIONt_nbd0.05836510
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.460
X-RAY DIFFRACTIONt_plane_restr0.0265

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