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- PDB-4z8x: Truncated FtsH from A. aeolicus -

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Basic information

Entry
Database: PDB / ID: 4z8x
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 / 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 / Resolution: 3.25 Å
AuthorsVostrukhina, M. / Baumann, U. / Schacherl, M. / Bieniossek, C. / Lanz, M. / Baumgartner, R.
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
DepositionApr 9, 2015Deposition 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)167,54411
Polymers166,2063
Non-polymers1,3398
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)335,08922
Polymers332,4116
Non-polymers2,67816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area22130 Å2
ΔGint-384 kcal/mol
Surface area117700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.860, 188.480, 206.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ATP-dependent zinc metalloprotease FtsH


Mass: 55401.848 Da / Num. of mol.: 3 / Fragment: residues 142-634 / Mutation: I250M, F360L, K552R, E627G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / 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: 4.35 Å3/Da / Density % sol: 71.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2 M ammonium sulphate, 2 mM EDTA, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→65 Å / Num. obs: 39332 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 128.49 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 17.6
Reflection shellResolution: 3.25→3.33 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.4 / % possible all: 96.4

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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: 3.25→64.51 Å / Cor.coef. Fo:Fc: 0.9158 / Cor.coef. Fo:Fc free: 0.9164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.403
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 2005 5.1 %Sphere
Rwork0.2261 ---
obs0.2275 39311 99.35 %-
Displacement parametersBiso mean: 221.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.3141 Å20 Å20 Å2
2--24.3067 Å20 Å2
3----24.6208 Å2
Refine analyzeLuzzati coordinate error obs: 0.469 Å
Refinement stepCycle: LAST / Resolution: 3.25→64.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10035 0 72 3 10110
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110249HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1113790HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4969SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes279HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1456HARMONIC5
X-RAY DIFFRACTIONt_it10249HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion3.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1359SEMIHARMONIC5
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_contact12012SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2422 156 5.59 %
Rwork0.2383 2633 -
all0.2385 2789 -
obs--96.72 %
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)
14.64670.07940.079112.5568-1.44142.21360.0211-0.2422-0.1684-0.1890.14290.52710.3994-0.1562-0.1640.1653-0.0390.09060.02640.18030.5876-22.2539-25.8938-54.9587
211.6834-3.2020.62035.7317-0.61381.82330.0641-0.0591-0.73520.1383-0.1236-0.00990.26240.18810.0595-0.12210.0483-0.0972-0.31690.17710.32411.1338-32.3615-54.783
38.27574.4879-0.78249.5746-0.39924.1292-0.134-0.08570.09630.19020.33521.0885-0.1588-0.8032-0.2012-0.29760.10310.2149-0.22340.06110.5819-33.68626.2644-54.3155
410.3574-5.78681.195516.63093.799216.6309-0.10320.51730.3784-0.45170.0728-0.25770.0866-0.28480.03050.55650.292-0.0780.53030.22320.5621-24.3735-26.7456-91.8068
516.6309-5.7513-0.04787.19412.914216.6309-0.03650.18750.5043-0.6452-0.02840.09740.1202-0.07520.06490.3128-0.0233-0.14540.60790.1880.501810.9763-34.4527-91.6302
611.70455.82085.393112.5377-1.449816.58320.02650.4928-0.1864-0.2618-0.2356-0.3174-0.1507-0.26590.20910.6079-0.29950.18080.45290.04250.4306-35.82957.9788-91.5594
74.5358-0.97682.28869.3058-0.94349.0342-0.03450.1715-0.4586-0.1921-0.0004-0.13730.1710.23590.03490.48590.28240.17030.1604-0.27930.2876-12.3807-53.0194-79.2038
88.5376-3.57330.33734.59720.28878.3999-0.00390.2346-0.1322-0.36060.0125-0.52620.00570.2519-0.00860.0990.25950.28060.4913-0.02820.258639.621-37.5792-78.7107
98.63131.9085-1.80098.3384-3.29228.6849-0.02010.1518-0.2592-0.05510.00940.16370.4033-0.19970.01070.36-0.2229-0.26860.3074-0.03540.3618-53.0511-15.0068-78.6465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|405 - A|608 }
2X-RAY DIFFRACTION2{ B|405 - B|608 }
3X-RAY DIFFRACTION3{ C|405 - C|606 }
4X-RAY DIFFRACTION4{ A|142 - A|322 }
5X-RAY DIFFRACTION5{ B|142 - B|322 }
6X-RAY DIFFRACTION6{ C|142 - C|322 }
7X-RAY DIFFRACTION7{ A|323 - A|398 }
8X-RAY DIFFRACTION8{ B|323 - B|398 }
9X-RAY DIFFRACTION9{ C|323 - C|398 }

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