[English] 日本語
Yorodumi
- PDB-3gpa: Crystal structure of the Mimivirus NDK N62L mutant complexed with CDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gpa
TitleCrystal structure of the Mimivirus NDK N62L mutant complexed with CDP
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 / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / 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
CYTIDINE-5'-DIPHOSPHATE / PHOSPHATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,46319
Polymers97,8036
Non-polymers2,66013
Water6,612367
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)100,55820
Polymers97,8036
Non-polymers2,75514
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)100,36818
Polymers97,8036
Non-polymers2,56512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Unit cell
Length a, b, c (Å)79.640, 152.421, 184.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 16300.550 Da / Num. of mol.: 6 / Mutation: N62L
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-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes 0.1M, 40 to 44% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2007 / Details: mirrors
RadiationMonochromator: Si(111) and Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→77 Å / Num. obs: 73214 / % possible obs: 96.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.052 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 6904 / Rsym value: 0.454 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIXrefinement
AMoREphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b8q

2b8q


Resolution: 2→70.446 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3668 5.01 %random
Rwork0.192 69546 --
obs0.194 73214 96.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.865 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 75.35 Å2 / Biso mean: 37.689 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.831 Å20 Å20 Å2
2---0.394 Å20 Å2
3----0.437 Å2
Refinement stepCycle: LAST / Resolution: 2→70.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6301 0 161 367 6829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076581
X-RAY DIFFRACTIONf_angle_d1.2168906
X-RAY DIFFRACTIONf_chiral_restr0.075982
X-RAY DIFFRACTIONf_plane_restr0.0041125
X-RAY DIFFRACTIONf_dihedral_angle_d21.9212482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0260.3311100.2852155226580
2.026-2.0540.3021040.2722320242483
2.054-2.0830.2821050.2612366247186
2.083-2.1150.3061110.2622450256189
2.115-2.1480.291450.2562523266892
2.148-2.1830.311390.2322629276897
2.183-2.220.2791480.21827502898100
2.22-2.2610.2851510.21727552906100
2.261-2.3040.2811600.20927152875100
2.304-2.3510.2521470.21427432890100
2.351-2.4020.2421300.2127802910100
2.402-2.4580.2741450.2072750289599
2.458-2.520.3121430.2182744288799
2.52-2.5880.2461260.2192750287699
2.588-2.6640.2481490.2112752290199
2.664-2.750.281520.2162742289499
2.75-2.8480.2541300.2182771290199
2.848-2.9630.2581410.2172762290399
2.963-3.0970.2961440.2192747289199
3.097-3.2610.2351330.192760289399
3.261-3.4650.2311670.1762776294399
3.465-3.7320.1881470.1662758290599
3.732-4.1080.1841670.1562746291399
4.108-4.7020.1721390.1412763290298
4.702-5.9240.1711640.1582766293098
5.924-70.490.1991710.1752773294494

+
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