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- PDB-2y78: Crystal structure of BPSS1823, a Mip-like chaperone from Burkhold... -

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Basic information

Entry
Database: PDB / ID: 2y78
TitleCrystal structure of BPSS1823, a Mip-like chaperone from Burkholderia pseudomallei
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASEProlyl isomerase
KeywordsISOMERASE / MIP / PPIASE / VIRULENCE
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 Å
AuthorsNorville, I.H. / O'Shea, K. / Sarkar-Tyson, M. / Harmer, N.J.
CitationJournal: Biochem.J. / Year: 2011
Title: The Structure of a Burkholderia Pseudomallei Immunophilin-Inhibitor Complex Reveals New Approaches to Antimicrobial Development
Authors: Norville, I.H. / O'Shea, K. / Sarkar-Tyson, M. / Zheng, S. / Titball, R.W. / Varani, G. / Harmer, N.J.
History
DepositionJan 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references / Version format compliance
Revision 1.2Aug 3, 2011Group: Derived calculations
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5256
Polymers14,1131
Non-polymers4125
Water4,936274
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
hetero molecules

A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,04912
Polymers28,2262
Non-polymers82410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1800 Å2
ΔGint-72.2 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.677, 54.677, 119.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2039-

HOH

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / Prolyl isomerase / PROLYL-PEPTIDE ISOMERASE


Mass: 14112.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: Q63J95, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.1 % / Description: NONE
Crystal growpH: 5.5 / Details: 1.1 M (NH4)2SO4, 0.05 M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.861
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 23, 2009 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 0.91→40.3 Å / Num. obs: 125244 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 8.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 0.91→0.96 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 88.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FKB AND 1ROT

1fkb

1rot


Resolution: 0.91→26.646 Å / SU ML: 0.08 / σ(F): 0.01 / Phase error: 8.42 / Stereochemistry target values: ML
Details: RESIDUES BEFORE GLYCINE -8 ARE DISORDERED. G-8 TO H0 ARE ORDERED.
RfactorNum. reflection% reflection
Rfree0.1161 6303 5 %
Rwork0.1094 --
obs0.1097 125244 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 0.91→26.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 23 274 1200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141068
X-RAY DIFFRACTIONf_angle_d1.5861474
X-RAY DIFFRACTIONf_dihedral_angle_d12.678421
X-RAY DIFFRACTIONf_chiral_restr0.098158
X-RAY DIFFRACTIONf_plane_restr0.01195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9102-0.94280.22675040.22929861X-RAY DIFFRACTION81
0.9428-0.98050.17066170.158411283X-RAY DIFFRACTION93
0.9805-1.02510.13386460.117711721X-RAY DIFFRACTION97
1.0251-1.07920.09666490.089311980X-RAY DIFFRACTION99
1.0792-1.14680.096110.079812107X-RAY DIFFRACTION99
1.1468-1.23540.09026320.077412141X-RAY DIFFRACTION99
1.2354-1.35970.08616450.079712201X-RAY DIFFRACTION99
1.3597-1.55640.09746440.081712314X-RAY DIFFRACTION100
1.5564-1.96080.09676900.088412401X-RAY DIFFRACTION100
1.9608-26.65780.13176650.129112932X-RAY DIFFRACTION100

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