[English] 日本語
Yorodumi
- PDB-2ve8: Xray structure of FtsK gamma domain (P. aeruginosa) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ve8
TitleXray structure of FtsK gamma domain (P. aeruginosa)
ComponentsDNA TRANSLOCASE FTSK
KeywordsTRANSPORT PROTEIN / NUCLEOTIDE-BINDING / CHROMOSOME PARTITION / ATP-BINDING / DNA-BINDING / TRANSLOCASE / WINGED HELIX / BACTERIAL CELL DIVISION / CELL DIVISION / TRANSMEMBRANE / INNER MEMBRANE / FTSZ / FTSK / MEMBRANE / CELL CYCLE / DNA BINDING
Function / homology
Function and homology information


cellular response to antibiotic / chromosome segregation / cell division / DNA binding / ATP binding / plasma membrane
Similarity search - Function
FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain / Ftsk_gamma / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. ...FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain / Ftsk_gamma / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA translocase FtsK
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLowe, J. / Allen, M.A. / Sherratt, D.J.
CitationJournal: Mol.Cell / Year: 2008
Title: Molecular Mechanism of Sequence-Directed DNA Loading and Translocation by Ftsk.
Authors: Lowe, J. / Ellonen, A. / Allen, M.D. / Atkinson, C. / Sherratt, D.J. / Grainge, I.
History
DepositionOct 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Advisory / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA TRANSLOCASE FTSK
B: DNA TRANSLOCASE FTSK
C: DNA TRANSLOCASE FTSK
D: DNA TRANSLOCASE FTSK
E: DNA TRANSLOCASE FTSK
F: DNA TRANSLOCASE FTSK
G: DNA TRANSLOCASE FTSK
H: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)63,4878
Polymers63,4878
Non-polymers00
Water11,908661
1
A: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)7,9361
Polymers7,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.494, 58.496, 95.408
Angle α, β, γ (deg.)90.00, 92.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
DNA TRANSLOCASE FTSK / FTSK


Mass: 7935.923 Da / Num. of mol.: 8 / Fragment: GAMMA DOMAIN, RESIDUES 739-811
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9I0M3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 21 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 95599 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5O

2j5o


Resolution: 1.4→95.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.963 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 4842 5 %RANDOM
Rwork0.144 ---
obs0.146 91374 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.02 Å2
2--0.78 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.4→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 0 661 4633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0224018
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3321.985421
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1935506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49922.308182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.361558
X-RAY DIFFRACTIONr_chiral_restr0.1710.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023050
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.22109
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22933
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2680.2442
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4361.52667
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.19824165
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.11231514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.8464.51256
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 376
Rwork0.174 6736

+
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