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- PDB-2r62: Crystal structure of Helicobacter pylori ATP dependent protease, FtsH -

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Basic information

Entry
Database: PDB / ID: 2r62
TitleCrystal structure of Helicobacter pylori ATP dependent protease, FtsH
ComponentsCell division protease ftsH homolog
KeywordsHYDROLASE / FtsH / 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 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 ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Cell division protease ftsH homolog
B: Cell division protease ftsH homolog


Theoretical massNumber of molelcules
Total (without water)58,2192
Polymers58,2192
Non-polymers00
Water00
1
A: Cell division protease ftsH homolog


Theoretical massNumber of molelcules
Total (without water)29,1091
Polymers29,1091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division protease ftsH homolog


Theoretical massNumber of molelcules
Total (without water)29,1091
Polymers29,1091
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.217, 141.217, 54.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Cell division protease ftsH homolog


Mass: 29109.320 Da / Num. of mol.: 2 / 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

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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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 17%(w/v) PEG 4000, 0.2M Li2SO4, 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: 3.2→50 Å / Num. all: 8963 / Num. obs: 8963 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 41.1
Reflection shellResolution: 3.2→3.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.7 / Num. unique all: 988 / Rsym value: 0.391 / % possible all: 99.3

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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: 0.915 / Cor.coef. Fo:Fc free: 0.879 / SU B: 90.49 / SU ML: 0.651 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.737 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Residue (B SER 306 ) and Residue (B GLU 307 ) are not linked: Distance of C-N bond is 1.64
RfactorNum. reflection% reflectionSelection details
Rfree0.33596 461 4.9 %RANDOM
Rwork0.28029 ---
all0.28283 8963 --
obs0.28283 8963 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 142.722 Å2
Baniso -1Baniso -2Baniso -3
1--3.75 Å2-1.88 Å20 Å2
2---3.75 Å20 Å2
3---5.63 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 0 0 3802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223854
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9845194
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.29825.227176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68715702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0041526
X-RAY DIFFRACTIONr_chiral_restr0.1020.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022896
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3140.22534
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.22702
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.360.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it14.1071.52527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it18.7923938
X-RAY DIFFRACTIONr_scbond_it0.98331442
X-RAY DIFFRACTIONr_scangle_it1.6954.51256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 30 -
Rwork0.403 666 -
obs--100 %
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)
12.84420.82941.37851.33020.65611.9096-0.2645-0.0574-0.22070.17770.15450.00370.39840.45540.1101-0.24410.11590.1129-0.3867-0.0367-0.2946-29.6454.8276-10.5391
24.88280.42920.02372.46032.44053.2154-0.62870.35060.1798-0.61070.4554-0.1841-0.4033-0.15730.1734-0.2344-0.1653-0.0988-0.32840.0171-0.3827-22.772237.5542-13.8249
33.4433-0.7684-2.19411.48191.00073.90.2057-0.4502-0.08910.26240.0256-0.23950.0670.0189-0.2313-0.36310.0029-0.0966-0.4867-0.0565-0.2214-47.235927.970514.5578
40.51970.2577-1.14511.2738-1.97364.2476-0.20770.1045-0.1401-0.1480.3977-0.1868-0.07840.3814-0.1899-0.47260.0959-0.0979-0.3079-0.30070.007-70.559914.7768-8.8945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA160 - 3401 - 181
2X-RAY DIFFRACTION2AA341 - 418182 - 259
3X-RAY DIFFRACTION3BB160 - 3401 - 181
4X-RAY DIFFRACTION4BB341 - 418182 - 259

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