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- PDB-4uog: Crystallographic structure of nucleoside diphosphate kinase from ... -

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Basic information

Entry
Database: PDB / ID: 4uog
TitleCrystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dCDP
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsTRANSFERASE / BINARY / COMPLEX / DCDP / PYRIMIDINE / BINDING SITE / DESOXYNUCLEOTIDE
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding
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
DEOXYCYTIDINE DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLopez-Zavala, A.A. / Stojanoff, V. / Rudino-Pinera, E. / Sotelo-Mundo, R.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of Nucleoside Diphosphate Kinase from Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates
Authors: Lopez-Zavala, A.A. / Quintero-Reyes, I.E. / Carrasco-Miranda, J.S. / Stojanoff, V. / Weichsel, A. / Rudino-Pinera, E. / Sotelo-Mundo, R.R.
History
DepositionJun 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,2819
Polymers51,0473
Non-polymers1,2346
Water5,747319
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,56318
Polymers102,0946
Non-polymers2,46912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area20950 Å2
ΔGint-163.5 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.160, 135.370, 104.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE


Mass: 17015.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Plasmid: PJEXPRESS414 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): SALT INDUCIBLE / References: UniProt: A5J299, nucleoside-diphosphate kinase
#2: Chemical ChemComp-YYY / DEOXYCYTIDINE DIPHOSPHATE


Mass: 387.177 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N3O10P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.4 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M AMMONIUM ACETATE, 0.1 M TRIS-HCL PH 8.5 AND 30% (V/V) 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 1, 2013 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→19.3 Å / Num. obs: 21500 / % possible obs: 95 % / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UOF

4uof


Resolution: 2.3→19.304 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1099 5.1 %
Rwork0.188 --
obs0.1915 21497 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25 Å2
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 75 319 3970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093732
X-RAY DIFFRACTIONf_angle_d1.1895046
X-RAY DIFFRACTIONf_dihedral_angle_d13.4081401
X-RAY DIFFRACTIONf_chiral_restr0.049534
X-RAY DIFFRACTIONf_plane_restr0.006633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.40480.35851320.28352605X-RAY DIFFRACTION98
2.4048-2.53130.31181440.25762581X-RAY DIFFRACTION98
2.5313-2.68950.28421540.2332590X-RAY DIFFRACTION99
2.6895-2.89650.311320.21892612X-RAY DIFFRACTION99
2.8965-3.18680.26651360.19762655X-RAY DIFFRACTION99
3.1868-3.64530.2441400.17162238X-RAY DIFFRACTION99
3.6453-4.58250.20591270.13892308X-RAY DIFFRACTION98
4.5825-19.30450.20721340.14372809X-RAY DIFFRACTION100

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