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- PDB-2r65: Crystal structure of Helicobacter pylori ATP dependent protease, ... -

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Basic information

Entry
Database: PDB / ID: 2r65
TitleCrystal structure of Helicobacter pylori ATP dependent protease, FtsH ADP complex
ComponentsCell division protease ftsH homolog
KeywordsHYDROLASE / FtsH / ADP / ATPase domain / Helicobacter pylori / ATP-binding / Cell cycle / Cell division / Membrane / Metal-binding / Metalloprotease / Nucleotide-binding / Protease / Transmembrane
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, 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, 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 / 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 / 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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKim, S.H. / Kang, G.B. / Song, H.-E. / Park, S.J. / Bae, M.-H. / Eom, S.H.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2008
Title: Structural studies on Helicobacter pyloriATP-dependent protease, FtsH
Authors: Kim, S.H. / Kang, G.B. / Song, H.-E. / Park, S.J. / Bea, M.-H. / Eom, S.H.
History
DepositionSep 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 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 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protease ftsH homolog
B: Cell division protease ftsH homolog
C: Cell division protease ftsH homolog
D: Cell division protease ftsH homolog
E: Cell division protease ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,68310
Polymers145,5475
Non-polymers2,1365
Water00
1
A: Cell division protease ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5372
Polymers29,1091
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division protease ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5372
Polymers29,1091
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cell division protease ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5372
Polymers29,1091
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cell division protease ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5372
Polymers29,1091
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cell division protease ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5372
Polymers29,1091
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.471, 219.485, 146.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Cell division protease ftsH homolog


Mass: 29109.320 Da / Num. of mol.: 5 / Fragment: ATPase domain, UNP residues 160-419 / Mutation: N170K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ftsH / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P71408, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES-NaOH pH 6.5, 17%(w/v) PEG 8000, 0.2M MgSO4, 0.01M ADP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 25338 / Num. obs: 25338 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 37.9
Reflection shellResolution: 3.3→3.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1260 / Rsym value: 0.342 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IXZ

1ixz


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.873 / SU B: 75.021 / SU ML: 0.59 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.688 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Residue (C ALA 389 ) and Residue (C LEU 390 ) are not linked : Distance of C-N bond is 1.62
RfactorNum. reflection% reflectionSelection details
Rfree0.33058 1366 5.1 %RANDOM
Rwork0.28762 ---
all0.28972 25338 --
obs0.28972 25338 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 128.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---8.56 Å20 Å2
3---8.97 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9510 0 135 0 9645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0229790
X-RAY DIFFRACTIONr_angle_refined_deg1.8222.00313225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99751235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.2125.227440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.728151755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6561565
X-RAY DIFFRACTIONr_chiral_restr0.1120.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027315
X-RAY DIFFRACTIONr_nbd_refined0.2850.25455
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2395
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.22
X-RAY DIFFRACTIONr_mcbond_it4.751.56356
X-RAY DIFFRACTIONr_mcangle_it6.26329860
X-RAY DIFFRACTIONr_scbond_it1.56733794
X-RAY DIFFRACTIONr_scangle_it2.5114.53365
LS refinement shellResolution: 3.3→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 101 -
Rwork0.385 1708 -
obs--93.83 %
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)
10.0539-0.3595-0.21492.39791.43664.10320.08610.107-0.1333-0.2441-0.44750.5644-0.4966-0.24590.3614-0.3128-0.1144-0.15340.0945-0.05210.200289.155945.325635.0531
22.9703-0.26972.02520.0681-0.17532.12840.7131-0.8264-0.19970.2352-0.266-0.15210.4176-0.5719-0.4471-0.071-0.3015-0.21550.10720.00890.077770.002328.882110.0874
31.69110.2489-1.1740.4845-0.09491.8543-0.0766-0.1701-0.0410.19540.10680.0279-0.12430.2035-0.0302-0.14820.0082-0.0195-0.02360.0080.163238.670217.53066.7732
41.1108-1.13090.42.4284-0.71340.775-0.1338-0.2526-0.16910.21880.3740.5114-0.1277-0.1105-0.2403-0.32580.06030.11620.03690.10370.141319.642-1.596929.8845
50.3571-0.84830.15382.2732-1.06791.97790.1956-0.1354-0.2260.18810.13470.28920.2553-0.4534-0.3304-0.3398-0.12870.00410.10570.06350.075529.0806-32.947644.9591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA160 - 4181 - 259
2X-RAY DIFFRACTION2BB160 - 4181 - 259
3X-RAY DIFFRACTION3CC160 - 4181 - 259
4X-RAY DIFFRACTION4DD160 - 4181 - 259
5X-RAY DIFFRACTION5EE160 - 4181 - 259

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