[English] 日本語
Yorodumi
- PDB-3fbc: Crystal structure of the Mimivirus NDK N62L-R107G double mutant c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fbc
TitleCrystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with dTDP
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / phosphotransferase nucleotide binding / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding
Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase-like domain superfamily / Nucleoside diphosphate kinase / Nucleoside diphosphate kinases active site.
Nucleoside diphosphate kinase
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJeudy, S. / Lartigue, A. / Claverie, J.M. / Abergel, C.
CitationJournal: J.Virol. / Year: 2009
Title: Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Authors: Jeudy, S. / Lartigue, A. / Claverie, J.M. / Abergel, C.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
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)100,33124
Polymers97,2026
Non-polymers3,12918
Water1,928107
1
A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,33124
Polymers97,2026
Non-polymers3,12918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules

B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,33124
Polymers97,2026
Non-polymers3,12918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Unit cell
γ
α
β
Length a, b, c (Å)80.387, 153.337, 185.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein/peptide
Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase / NDP kinase / NDK


Mass: 16200.407 Da / Num. of mol.: 6 / Mutation: N62L, R107G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R418, NDK / Plasmid: pDIGS02 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q5UQL3, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Magnesium
#3: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Thymidine diphosphate
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4 / Phosphate
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 40-44% MPD, 0.1M MOPS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2007 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→48.2 Å / Num. obs: 35512 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 63.066 Å2 / Rsym value: 0.087 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4754 / Rsym value: 0.406 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b8p
Resolution: 2.6→48.112 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1753 4.94 %random
Rwork0.189 33759 --
Obs0.192 35512 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.911 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 124.37 Å2 / Biso mean: 52.179 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.632 Å2-0 Å20 Å2
2---2.699 Å20 Å2
3---1.067 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 186 107 6555
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0086561
f_angle_d1.1868885
f_chiral_restr0.073973
f_plane_restr0.0041118
f_dihedral_angle_d21.2572455
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.670.3241440.26825242668100
2.67-2.7490.3181210.2525922713100
2.749-2.8380.3231400.23425582698100
2.838-2.9390.3381270.22925662693100
2.939-3.0570.2871240.2325992723100
3.057-3.1960.2961250.22126022727100
3.196-3.3640.2811450.20125792724100
3.364-3.5750.2791330.19625852718100
3.575-3.8510.2351200.18826222742100
3.851-4.2380.1931320.16326132745100
4.238-4.8510.1941390.1426172756100
4.851-6.110.2171520.16126382790100
6.11-48.120.2131510.172664281597

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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