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- PDB-6gco: Truncated FtsH from A. aeolicus in P312 -

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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, FtsH / Peptidase M41 / 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, FtsH / Peptidase M41 / 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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.

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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

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Phasing

PhasingMethod: molecular replacement

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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

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