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- PDB-4ww0: Truncated FtsH from A. aeolicus -

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Basic information

Entry
Database: PDB / ID: 4ww0
TitleTruncated FtsH from A. aeolicus
ComponentsATP-dependent zinc metalloprotease FtsH
KeywordsHYDROLASE / FtsH / metalloprotease / ATP / intracellular protein degradation
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / Resolution: 2.96 Å
AuthorsVostrukhina, M. / Baumann, U. / Schacherl, M. / Bieniossek, C. / Lanz, M. / Baumgartner, R.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-120174 Switzerland
Swiss National Science Foundation3100A0-108262 Switzerland
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer.
Authors: Vostrukhina, M. / Popov, A. / Brunstein, E. / Lanz, M.A. / Baumgartner, R. / Bieniossek, C. / Schacherl, M. / Baumann, U.
History
DepositionNov 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)167,6839
Polymers166,2063
Non-polymers1,4786
Water543
1
A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)335,36718
Polymers332,4116
Non-polymers2,95612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area28150 Å2
ΔGint-296 kcal/mol
Surface area108430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.230, 162.260, 170.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein ATP-dependent zinc metalloprotease FtsH


Mass: 55401.848 Da / Num. of mol.: 3 / Fragment: UNP residues 142-634 / Mutation: I250M, F360L,K553R, E627G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: ftsH, aq_936 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: O67077, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60 % Tacsimate pH 7.0, 10 mM AMP-PNP / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 39488 / % possible obs: 97.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 87.01 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.1
Reflection shellResolution: 2.96→3.03 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1 / % possible all: 91.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DI4, 2CE7

2di4

2ce7


Resolution: 2.96→43.01 Å / Cor.coef. Fo:Fc: 0.9448 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.324 / SU Rfree Blow DPI: 0.359
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1972 5 %RANDOM
Rwork0.2088 ---
obs0.2107 39476 98.25 %-
Displacement parametersBiso mean: 112.03 Å2
Baniso -1Baniso -2Baniso -3
1--2.8218 Å20 Å20 Å2
2--10.1247 Å20 Å2
3----7.3029 Å2
Refine analyzeLuzzati coordinate error obs: 0.626 Å
Refinement stepCycle: LAST / Resolution: 2.96→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9891 0 84 3 9978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910119HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1213616HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4907SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes273HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1451HARMONIC5
X-RAY DIFFRACTIONt_it10119HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion3.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1340SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle18HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11873SEMIHARMONIC4
LS refinement shellResolution: 2.96→3.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2884 133 4.8 %
Rwork0.2611 2636 -
all0.2624 2769 -
obs--98.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.00941.7386-2.00384.2662-2.19456.6007-0.28960.03650.0638-0.72450.10850.01740.7832-0.21580.1811-0.0434-0.00320.0896-0.293-0.0389-0.3128-35.170619.156314.267
27.10660.21380.73032.610.13481.6481-0.0482-0.0532-0.16360.1151-0.02150.02650.0041-0.38290.06970.0149-0.01590.1863-0.1587-0.0463-0.1886-27.056521.065748.8365
32.74431.48790.23066.82821.10314.80820.0264-0.2-0.2967-0.6613-0.2651-0.4580.88180.34720.23870.16630.0258-0.1212-0.33790.017-0.479734.021522.629417.1945
42.37061.0431-0.06466.766-0.19162.4564-0.0895-0.0669-0.0029-0.090.1394-0.28430.00330.4132-0.0499-0.1637-0.0627-0.1464-0.1606-0.0805-0.059131.57913.257347.9813
59.8584-4.8864-0.51568.1433.82673.5810.15730.8645-0.4707-0.0010.7372-0.0699-0.22421.0671-0.8945-0.37210.06580.03060.0787-0.304-0.3726-1.265631.059619.6192
66.1867-2.26630.59554.3876-0.66481.20850.0122-0.07780.65720.4108-0.0923-0.4105-0.32390.05560.08-0.0366-0.08490.0341-0.3016-0.1131-0.04224.755533.804449.6207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|142 - A|405 }
2X-RAY DIFFRACTION2{ A|406 - A|607 }
3X-RAY DIFFRACTION3{ B|142 - B|405 }
4X-RAY DIFFRACTION4{ B|406 - B|607 }
5X-RAY DIFFRACTION5{ C|146 - C|405 }
6X-RAY DIFFRACTION6{ C|406 - C|607 }

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