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- PDB-5jhe: The Crystal Structure of the Saccharomyces cerevisiae Co-Chaperon... -

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Basic information

Entry
Database: PDB / ID: 5jhe
TitleThe Crystal Structure of the Saccharomyces cerevisiae Co-Chaperone Cpr7
ComponentsPeptidyl-prolyl cis-trans isomerase CYP7
KeywordsCHAPERONE / cochaperone
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / protein folding / protein refolding / cytoplasm / cytosol
Similarity search - Function
Cyclophilin-like / Cyclophilin / Tetratricopeptide repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / TPR repeat region circular profile. ...Cyclophilin-like / Cyclophilin / Tetratricopeptide repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase CYP7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYu, Q. / Xu, L.
Funding support China, 4items
OrganizationGrant numberCountry
Chinese National Natural Science Foundation31130018 China
Ministry of Science and Technology (China)2012CB917200 China
Chinese National Natural Science Foundation31370732 China
Scientific Research Grant of Hefei Science Center of CAS2015SRG-HSC042 China
CitationJournal: To Be Published
Title: The Crystal Structure of the Saccharomyces cerevisiae Co-Chaperone Cpr7
Authors: Yu, Q. / Xu, L.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 8, 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: Peptidyl-prolyl cis-trans isomerase CYP7


Theoretical massNumber of molelcules
Total (without water)45,7371
Polymers45,7371
Non-polymers00
Water6,197344
1
A: Peptidyl-prolyl cis-trans isomerase CYP7

A: Peptidyl-prolyl cis-trans isomerase CYP7


Theoretical massNumber of molelcules
Total (without water)91,4752
Polymers91,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)75.332, 75.332, 100.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase CYP7 / PPIase CYP7 / Rotamase CYP7


Mass: 45737.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: CPR7, YJR032W, J1585 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P47103, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% (w/v) PEG 8000, 0.1M Ca acetate, 0.1M Na cacodylate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 51730 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IHG

1ihg


Resolution: 1.8→41.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21082 2574 5.1 %RANDOM
Rwork0.1846 ---
obs0.18597 48023 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.724 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0 Å2
2--0.24 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.8→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 0 344 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193151
X-RAY DIFFRACTIONr_bond_other_d00.022936
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9594249
X-RAY DIFFRACTIONr_angle_other_deg3.65436764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39224.873158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61115553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9861515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023605
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02732
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_it1.9092.9851550
X-RAY DIFFRACTIONr_mcbond_other1.9062.9831549
X-RAY DIFFRACTIONr_mcangle_it3.0794.4671934
X-RAY DIFFRACTIONr_mcangle_other3.0784.4681935
X-RAY DIFFRACTIONr_scbond_it2.5813.2831601
X-RAY DIFFRACTIONr_scbond_other2.583.2841602
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0984.82316
X-RAY DIFFRACTIONr_long_range_B_refined6.30524.8313833
X-RAY DIFFRACTIONr_long_range_B_other6.02724.0363639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 185 -
Rwork0.242 3518 -
obs--97.32 %

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