[English] 日本語
Yorodumi
- PDB-6gco: Truncated FtsH from A. aeolicus in P312 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gco
TitleTruncated FtsH from A. aeolicus in P312
ComponentsATP-dependent zinc metalloprotease FtsH
KeywordsHYDROLASE / AAA protease / zinc metalloprotease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane
Similarity search - Function
Peptidase M41 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Peptidase M41 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.323 Å
AuthorsUthoff, M. / Baumann, U.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Conformational flexibility of pore loop-1 gives insights into substrate translocation by the AAA+protease FtsH.
Authors: Uthoff, M. / Baumann, U.
History
DepositionApr 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2586
Polymers106,2732
Non-polymers9854
Water00
1
A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
hetero molecules

A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
hetero molecules

A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,77318
Polymers318,8186
Non-polymers2,95612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_965-y+4,x-y+1,z1
crystal symmetry operation3_895-x+y+3,-x+4,z1
Unit cell
Length a, b, c (Å)117.304, 117.304, 137.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 151 through 153 and (name N...
21(chain B and ((resid 151 through 153 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHR(chain A and ((resid 151 through 153 and (name N...AA151 - 15322 - 24
12ADPADP(chain A and ((resid 151 through 153 and (name N...AA - C151 - 70122
13ADPADP(chain A and ((resid 151 through 153 and (name N...AA - C151 - 70122
14ADPADP(chain A and ((resid 151 through 153 and (name N...AA - C151 - 70122
15ADPADP(chain A and ((resid 151 through 153 and (name N...AA - C151 - 70122
21THRTHR(chain B and ((resid 151 through 153 and (name N...BB151 - 15322 - 24
22CYSCYS(chain B and ((resid 151 through 153 and (name N...BB151 - 60622 - 477
23CYSCYS(chain B and ((resid 151 through 153 and (name N...BB151 - 60622 - 477
24CYSCYS(chain B and ((resid 151 through 153 and (name N...BB151 - 60622 - 477
25CYSCYS(chain B and ((resid 151 through 153 and (name N...BB151 - 60622 - 477

-
Components

#1: Protein ATP-dependent zinc metalloprotease FtsH


Mass: 53136.293 Da / Num. of mol.: 2
Fragment: cytosolic Part (AAA+ and protease) with truncated C-terminus
Mutation: deleted 1-151, 608-634 inserted N-terminal His tag and thrombin cleavage site
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: ftsH, aq_936 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus RIPL
References: UniProt: O67077, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 % / Description: Hexagonal plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 0.2 M KCl, 0.05 M HEPES/NaOH pH7.75, 33% pentaerythritol propoxylate 426 The affinity tag was cleaved by thrombin. This cleavage was just partial according to a SDS-PAGE analysis.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.44
ReflectionResolution: 3.32→81.613 Å / Num. obs: 15949 / % possible obs: 98.8 % / Redundancy: 10.04 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.104 / Χ2: 1.046 / Net I/σ(I): 18.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.32-3.529.4691.0712.1823900.7291.13192.5
3.52-3.779.9510.5984.2324360.8960.631100
3.77-4.0710.1670.3177.8622480.9740.334100
4.07-4.4610.7430.18613.4420850.9890.195100
4.46-4.9810.4810.12319.0419020.9960.13100
4.98-5.759.7490.1120.6916760.9950.116100
5.75-7.0310.340.07729.9614280.9980.081100
7.03-9.99.7920.03660.711280.9990.038100
9.9-81.6139.020.02579.496560.9990.02799.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4ww0

4ww0


Resolution: 3.323→81.613 Å / Cross valid method: THROUGHOUT / σ(F): 177.68 / Phase error: 42.51
Details: Phased via molecular replacement with 4ww0, fragments copied over from R32 version
RfactorNum. reflection% reflection
Rfree0.2654 1120 7.02 %
Rwork0.2404 --
obs0.2491 15948 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 378.7 Å2 / Biso mean: 158.0409 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 3.323→81.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 80 0 5378
Biso mean--214.56 --
Num. residues----804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035438
X-RAY DIFFRACTIONf_angle_d0.6497455
X-RAY DIFFRACTIONf_chiral_restr0.043906
X-RAY DIFFRACTIONf_plane_restr0.004986
X-RAY DIFFRACTIONf_dihedral_angle_d10.2223203
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3260X-RAY DIFFRACTION7.775TORSIONAL
12B3260X-RAY DIFFRACTION7.775TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3263-3.47770.31311350.31861703183885
3.4777-3.6610.29941410.32791846198793
3.661-3.89030.28541400.29331840198093
3.8903-4.19060.27761450.26841870201593
4.1906-4.61220.33231370.27231849198693
4.6122-5.27910.251380.25121867200593
5.2791-6.64950.30281380.26651893203193
6.6495-56.81850.2431440.19381944208893

+
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://pdbjlvh1.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