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- PDB-8hm4: Crystal structure of PPIase -

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Basic information

Entry
Database: PDB / ID: 8hm4
TitleCrystal structure of PPIase
ComponentsPeptidylprolyl isomerase
KeywordsISOMERASE / CHAPERONE
Function / homologyTrigger factor/SurA domain superfamily / 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 / peptidyl-prolyl cis-trans isomerase activity / PpiC domain-containing protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å
AuthorsXu, J.H. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122007 China
CitationJournal: Nat Microbiol / Year: 2024
Title: Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome.
Authors: Jiang, K. / Li, W. / Tong, M. / Xu, J. / Chen, Z. / Yang, Y. / Zang, Y. / Jiao, X. / Liu, C. / Lim, B. / Jiang, X. / Wang, J. / Wu, D. / Wang, M. / Liu, S.J. / Shao, F. / Gao, X.
History
DepositionDec 2, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidylprolyl isomerase
B: Peptidylprolyl isomerase


Theoretical massNumber of molelcules
Total (without water)98,5362
Polymers98,5362
Non-polymers00
Water00
1
A: Peptidylprolyl isomerase


Theoretical massNumber of molelcules
Total (without water)49,2681
Polymers49,2681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidylprolyl isomerase


Theoretical massNumber of molelcules
Total (without water)49,2681
Polymers49,2681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.425, 126.087, 130.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 33 through 148 or resid 155 through 453))
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALLEUA4 - 119
d_12ens_1THRILEA126 - 424
d_21ens_1VALILEB1 - 415

NCS oper: (Code: givenMatrix: (-0.998560204313, 0.0368004218624, -0.0390288010818), (0.00127226197204, -0.711120178755, -0.703069322839), (-0.0536274156808, -0.702106701519, 0.710049491211)Vector: 46. ...NCS oper: (Code: given
Matrix: (-0.998560204313, 0.0368004218624, -0.0390288010818), (0.00127226197204, -0.711120178755, -0.703069322839), (-0.0536274156808, -0.702106701519, 0.710049491211)
Vector: 46.0058495041, -54.3195109839, -22.7901268393)

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Components

#1: Protein Peptidylprolyl isomerase


Mass: 49268.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: BN669_00367 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R6ZJY1
Has protein modificationY

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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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate, 0.1M sodium chloride, 0.2M ammonium sulfate, 20% PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.79→37.44 Å / Num. obs: 13967 / % possible obs: 99.32 % / Redundancy: 6.6 % / Biso Wilson estimate: 159.1 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.038 / Net I/σ(I): 15.6
Reflection shellResolution: 3.79→3.93 Å / Num. unique obs: 1342 / CC1/2: 0.608 / Rpim(I) all: 0.397

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.19.2_4158refinement
HKL-3000data reduction
MOLREPphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.79→37.44 Å / SU ML: 0.6805 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.0147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3016 1395 10.01 %
Rwork0.2843 12546 -
obs0.2861 13941 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 206.96 Å2
Refinement stepCycle: LAST / Resolution: 3.79→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6807 0 0 0 6807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01296918
X-RAY DIFFRACTIONf_angle_d1.33679322
X-RAY DIFFRACTIONf_chiral_restr0.06761023
X-RAY DIFFRACTIONf_plane_restr0.00921224
X-RAY DIFFRACTIONf_dihedral_angle_d4.9557919
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 5.45990744546 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.79-3.930.40111310.36061206X-RAY DIFFRACTION96.6
3.93-4.090.39181370.30811229X-RAY DIFFRACTION99.49
4.09-4.270.32831320.27461218X-RAY DIFFRACTION99.7
4.27-4.50.31991410.25671244X-RAY DIFFRACTION99.86
4.5-4.780.31471410.26221247X-RAY DIFFRACTION99.93
4.78-5.150.3191400.27831246X-RAY DIFFRACTION99.86
5.15-5.660.37381400.34421252X-RAY DIFFRACTION99.93
5.66-6.480.3761350.34481273X-RAY DIFFRACTION99.86
6.48-8.150.32831440.30991285X-RAY DIFFRACTION100
8.15-37.440.22851540.24661346X-RAY DIFFRACTION99.47

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