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- PDB-6bhf: Crystal structure of the petidylprolyl cis,trans-isomerase from H... -

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Basic information

Entry
Database: PDB / ID: 6bhf
TitleCrystal structure of the petidylprolyl cis,trans-isomerase from Helicobacter pylori
ComponentsPutative peptidyl-prolyl cis-trans isomerase HP_0175
KeywordsISOMERASE / Parvulin PPIase TLR4-agonist
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
: / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Putative peptidyl-prolyl cis-trans isomerase HP_0175
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYaseen, A. / Audette, G.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural flexibility in the Helicobacter pylori peptidyl-prolyl cis,trans-isomerase HP0175 is achieved through an extension of the chaperone helices.
Authors: Yaseen, A. / Audette, G.F.
History
DepositionOct 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative peptidyl-prolyl cis-trans isomerase HP_0175


Theoretical massNumber of molelcules
Total (without water)34,1191
Polymers34,1191
Non-polymers00
Water1,02757
1
A: Putative peptidyl-prolyl cis-trans isomerase HP_0175

A: Putative peptidyl-prolyl cis-trans isomerase HP_0175


Theoretical massNumber of molelcules
Total (without water)68,2382
Polymers68,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area4470 Å2
ΔGint-31 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.951, 90.951, 67.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative peptidyl-prolyl cis-trans isomerase HP_0175 / PPIase HP_0175 / Rotamase HP_0175


Mass: 34119.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_0175 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56112, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe structure has a Thr at position 80 of chain A. This is both confirmed by the electron density ...The structure has a Thr at position 80 of chain A. This is both confirmed by the electron density and sequencing of the crystallized construct

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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: 2.35 Å3/Da / Density % sol: 47.58 % / Description: hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES (pH 7.0), 30% (v/v) Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→45.5 Å / Num. obs: 19446 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 38.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.039 / Rrim(I) all: 0.089 / Net I/σ(I): 15.2
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.515 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1459 / CC1/2: 0.786 / Rpim(I) all: 0.73 / Rrim(I) all: 1.69 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ez1

5ez1


Resolution: 2.09→45.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 21.04 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27526 959 4.9 %RANDOM
Rwork0.2143 ---
obs0.21746 18461 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.784 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20.79 Å20 Å2
2--1.59 Å2-0 Å2
3----5.15 Å2
Refinement stepCycle: 1 / Resolution: 2.09→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 57 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192037
X-RAY DIFFRACTIONr_bond_other_d0.0020.021934
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9682736
X-RAY DIFFRACTIONr_angle_other_deg1.12234526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27526.06199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95515406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.45158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212228
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02368
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9984.701996
X-RAY DIFFRACTIONr_mcbond_other2.9964.7995
X-RAY DIFFRACTIONr_mcangle_it4.2617.0391242
X-RAY DIFFRACTIONr_mcangle_other4.267.041243
X-RAY DIFFRACTIONr_scbond_it3.8825.2161041
X-RAY DIFFRACTIONr_scbond_other3.8825.2161041
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0547.6011492
X-RAY DIFFRACTIONr_long_range_B_refined7.50656.4692368
X-RAY DIFFRACTIONr_long_range_B_other7.50856.4572362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.085→2.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 85 -
Rwork0.414 1305 -
obs--99.43 %
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)
10.53290.1283-0.11930.2966-0.00120.03470.034-0.1261-0.10530.0038-0.07020.0595-0.03420.03370.03630.18260.0062-0.01910.14890.01510.0488-3.733569.37545.3981
20.22870.1813-0.02830.2236-0.07390.1180.0358-0.1354-0.1368-0.0852-0.0742-0.08410.04980.02420.03850.188-0.0549-0.02940.13660.07450.11921.457667.47232.5803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 60
2X-RAY DIFFRACTION1A69 - 101
3X-RAY DIFFRACTION1A102 - 139
4X-RAY DIFFRACTION1A140 - 153
5X-RAY DIFFRACTION1A154 - 261
6X-RAY DIFFRACTION1A262 - 292
7X-RAY DIFFRACTION1A293 - 299
8X-RAY DIFFRACTION2W1 - 57

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