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- PDB-2dhr: Whole cytosolic region of ATP-dependent metalloprotease FtsH (G399L) -

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Basic information

Entry
Database: PDB / ID: 2dhr
TitleWhole cytosolic region of ATP-dependent metalloprotease FtsH (G399L)
ComponentsFtsH
KeywordsHYDROLASE / AAA+ protein / hexameric Zn 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 / ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.9 Å
AuthorsSuno, R. / Niwa, H. / Tsuchiya, D. / Zhang, X. / Yoshida, M. / Morikawa, K.
Citation
Journal: Mol.Cell / Year: 2006
Title: Structure of the Whole Cytosolic Region of ATP-Dependent Protease FtsH
Authors: Suno, R. / Niwa, H. / Tsuchiya, D. / Zhang, X. / Yoshida, M. / Morikawa, K.
#1: Journal: Structure / Year: 2002
Title: Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8
Authors: Niwa, H. / Tsuchiya, D. / Makyio, H. / Yoshida, M. / Morikawa, K.
History
DepositionMar 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FtsH
B: FtsH
C: FtsH
D: FtsH
E: FtsH
F: FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,77912
Polymers332,2166
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28370 Å2
ΔGint-95 kcal/mol
Surface area129190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.153, 146.153, 349.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a hexamer composed of the six polypeptide chains in the asymmetric unit.

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Components

#1: Protein
FtsH / ATP-dependent metalloprotease


Mass: 55369.281 Da / Num. of mol.: 6 / Fragment: whole cytosolic region / Mutation: G399L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LCZ4, UniProt: Q5SI82*PLUS
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M Tris-HCl, 1% PEG8K, 0.2mM Zn acetate, 2.5mM ADP, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→100 Å / Num. all: 40304 / Num. obs: 40304 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077
Reflection shellResolution: 3.9→4.1 Å / Rmerge(I) obs: 0.547 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 3.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.342 1921 RANDOM
Rwork0.299 --
all0.301 36530 -
obs0.301 36530 -
Refinement stepCycle: LAST / Resolution: 3.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21298 0 162 0 21460

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