[English] 日本語
Yorodumi
- PDB-2hur: Escherichia coli nucleoside diphosphate kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hur
TitleEscherichia coli nucleoside diphosphate kinase
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsSIGNALING PROTEIN / TRANSFERASE / TYPE II TETRAMER
Function / homology
Function and homology information


purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMoynie, L. / Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
Citation
Journal: Proteins / Year: 2007
Title: The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family
Authors: Moynie, L. / Giraud, M.-F. / Georgescauld, F. / Lascu, I. / Dautant, A.
#1: Journal: J.Bacteriol. / Year: 1995
Title: Nucleoside diphosphate kinase from Escherichia coli
Authors: Almaula, N. / Lu, Q. / Delgado, J. / Belkin, S. / Inouye, M.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 A resolution
Authors: Williams, R.L. / Oren, D.A. / Inouye, S. / Inouye, M. / Arnold, E.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8 A resolution.
Authors: LeBras, G. / Lascu, I. / Lacombe, M.L. / Janin, J.
History
DepositionJul 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,67812
Polymers92,1016
Non-polymers5766
Water12,917717
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7858
Polymers61,4014
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7858
Polymers61,4014
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
3
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8934
Polymers30,7002
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-92 kcal/mol
Surface area23520 Å2
MethodPQS
4
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8934
Polymers30,7002
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-91 kcal/mol
Surface area22460 Å2
MethodPQS
5
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8934
Polymers30,7002
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)118.904, 76.095, 104.588
Angle α, β, γ (deg.)90.00, 112.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-261-

HOH

21B-296-

HOH

31B-297-

HOH

41C-219-

HOH

51E-303-

HOH

61F-280-

HOH

71F-323-

HOH

-
Components

#1: Protein
NUCLEOSIDE DIPHOSPHATE KINASE / E.C.2.7.4.6 / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 15350.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ndk / Plasmid: PJC20 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A763, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M AMMONIUM SULPHATE, 25% PEG 4000 0.1 M SODIUM ACETATE/ACETIC ACID, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.62→38.05 Å / Num. all: 108681 / Num. obs: 108681 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.09 / Net I/σ(I): 16.6
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.38 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB FILE 2NCK

2nck


Resolution: 1.62→38.05 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2343463.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 5451 5 %RANDOM
Rwork0.191 ---
all0.196 108681 --
obs0.191 108681 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0217 Å2 / ksol: 0.368627 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å23.96 Å2
2--1.33 Å20 Å2
3----0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.62→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 30 717 7239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 894 5 %
Rwork0.263 16974 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more