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

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Basic information

Entry
Database: PDB / ID: 4uof
TitleCrystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dADP
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsTRANSFERASE / BINARY / COMPLEX / DADP / PURINE / WHITE-SHRIMP / 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 (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
2'-DEOXYADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 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 the Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates
Authors: Lopez-Zavala, A.A. / Quintero-Reyez, 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 1.1Feb 25, 2015Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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)52,3539
Polymers51,0473
Non-polymers1,3076
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-25.7 kcal/mol
Surface area24500 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.110, 134.380, 104.760
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-DAT / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / DADP


Mass: 411.202 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O9P2
#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.: 301 / 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: 49.2 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% (W/V) PEG 4,000

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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: 2.1→19.8 Å / Num. obs: 26320 / % possible obs: 91.2 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 20.42 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.7 / % possible all: 95.1

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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 1BE4

1be4


Resolution: 2.102→19.854 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 1334 5.1 %
Rwork0.1895 --
obs0.1926 26423 90.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.8 Å2
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 2.102→19.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 81 301 3961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023749
X-RAY DIFFRACTIONf_angle_d1.3945064
X-RAY DIFFRACTIONf_dihedral_angle_d14.7751404
X-RAY DIFFRACTIONf_chiral_restr0.067534
X-RAY DIFFRACTIONf_plane_restr0.007633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1022-2.17720.29911490.24292601X-RAY DIFFRACTION96
2.1772-2.26430.4207670.36841283X-RAY DIFFRACTION70
2.2643-2.36710.31391410.25422397X-RAY DIFFRACTION95
2.3671-2.49170.29381460.22632732X-RAY DIFFRACTION100
2.4917-2.64750.30921370.22782750X-RAY DIFFRACTION100
2.6475-2.85140.28571440.21722745X-RAY DIFFRACTION100
2.8514-3.13730.27511730.1982742X-RAY DIFFRACTION100
3.1373-3.5890.20871320.17552798X-RAY DIFFRACTION100
3.589-4.51290.17131090.13572127X-RAY DIFFRACTION76
4.5129-19.85530.19211360.13382914X-RAY DIFFRACTION100

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