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- PDB-4fru: Crystal structure of horse wild-type cyclophilin B -

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Basic information

Entry
Database: PDB / ID: 4fru
TitleCrystal structure of horse wild-type cyclophilin B
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / cyclophilin-type PPIase / Peptidyl-prolyl cis-trans isomerase / chaperone / foldase / P3H1-CRTAP-CypB complex / LH1 binding / endoplasmic reticulum
Function / homology
Function and homology information


protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein-containing complex / metal ion binding
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsBoudko, S.P. / Ishikawa, Y. / Bachinger, H.P.
CitationJournal: BMC Res Notes / Year: 2012
Title: Crystal structures of wild-type and mutated cyclophilin B that causes hyperelastosis cutis in the American quarter horse.
Authors: Boudko, S.P. / Ishikawa, Y. / Lerch, T.F. / Nix, J. / Chapman, M.S. / Bachinger, H.P.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Mar 13, 2013Group: Refinement description
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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)20,8515
Polymers20,4661
Non-polymers3854
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.880, 44.070, 60.570
Angle α, β, γ (deg.)90.00, 95.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-492-

HOH

21A-554-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / CYCLOPHILIN B


Mass: 20465.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: PPIB / Plasmid: pET30b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5YBL8, peptidylprolyl isomerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ME2 / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M MES, 10mM ZnCl2, 10% glycerol, 28% PEG MME 550, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.827 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 12, 2010
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.1→16.42 Å / Num. all: 69023 / Num. obs: 62397 / % possible obs: 90.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 4.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.8
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3.9 / % possible all: 53.4

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Processing

Software
NameVersionClassification
AMoREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CYN

1cyn


Resolution: 1.1→16.416 Å / SU ML: 0.07 / σ(F): 1.37 / Phase error: 11.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1391 3161 5.07 %
Rwork0.1155 --
obs0.1167 62351 90.22 %
all-69108 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→16.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 17 283 1729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071521
X-RAY DIFFRACTIONf_angle_d1.3012041
X-RAY DIFFRACTIONf_dihedral_angle_d11.819588
X-RAY DIFFRACTIONf_chiral_restr0.078218
X-RAY DIFFRACTIONf_plane_restr0.006260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11640.1861560.2131248X-RAY DIFFRACTION43
1.1164-1.13390.1995810.19191449X-RAY DIFFRACTION52
1.1339-1.15240.2159920.17641695X-RAY DIFFRACTION59
1.1524-1.17230.2102950.16581897X-RAY DIFFRACTION68
1.1723-1.19360.19251040.16092212X-RAY DIFFRACTION77
1.1936-1.21660.17331480.14552410X-RAY DIFFRACTION86
1.2166-1.24140.19121470.13462605X-RAY DIFFRACTION92
1.2414-1.26840.16741630.12232781X-RAY DIFFRACTION97
1.2684-1.29790.12931420.10722824X-RAY DIFFRACTION100
1.2979-1.33030.13531150.09962863X-RAY DIFFRACTION100
1.3303-1.36630.12941470.0972871X-RAY DIFFRACTION100
1.3663-1.40640.11821790.09132815X-RAY DIFFRACTION100
1.4064-1.45180.12871650.08812831X-RAY DIFFRACTION100
1.4518-1.50370.10991630.08842838X-RAY DIFFRACTION100
1.5037-1.56380.12851690.08562846X-RAY DIFFRACTION100
1.5638-1.63490.11391530.08742843X-RAY DIFFRACTION100
1.6349-1.72110.10721390.08982837X-RAY DIFFRACTION100
1.7211-1.82880.10721690.0922857X-RAY DIFFRACTION100
1.8288-1.96970.12411510.09642873X-RAY DIFFRACTION100
1.9697-2.16760.11521290.0982894X-RAY DIFFRACTION100
2.1676-2.48030.13011540.10852858X-RAY DIFFRACTION100
2.4803-3.12140.15451550.13012885X-RAY DIFFRACTION100
3.1214-16.41810.14831450.13912958X-RAY DIFFRACTION100

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