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- PDB-4frv: Crystal structure of mutated cyclophilin B that causes hyperelast... -

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Basic information

Entry
Database: PDB / ID: 4frv
TitleCrystal structure of mutated cyclophilin B that causes hyperelastosis cutis in the American Quarter Horse
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)20,9515
Polymers20,5661
Non-polymers3854
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.790, 44.160, 60.110
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-467-

HOH

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Components

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


Mass: 20565.660 Da / Num. of mol.: 1 / Mutation: G39R
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.: 276 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICT IS INDICATED AS HYPERELASTOSIS CUTIS MUTATION SINCE IT WAS CLONED DIRECTLY FROM AN AFFECTED HORSE

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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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growMethod: 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

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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→16.29 Å / Num. all: 68567 / Num. obs: 61849 / % possible obs: 90.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 4.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.4
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.2 / % 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→16.286 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 12.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.138 3083 4.99 %
Rwork0.1194 --
obs0.1204 61728 89.97 %
all-68612 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→16.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 17 276 1731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071530
X-RAY DIFFRACTIONf_angle_d1.2862052
X-RAY DIFFRACTIONf_dihedral_angle_d11.606595
X-RAY DIFFRACTIONf_chiral_restr0.074219
X-RAY DIFFRACTIONf_plane_restr0.006261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11720.1902760.19961311X-RAY DIFFRACTION44
1.1172-1.13550.1978840.17881464X-RAY DIFFRACTION50
1.1355-1.15510.1722690.17141806X-RAY DIFFRACTION60
1.1551-1.17610.15571140.16181976X-RAY DIFFRACTION68
1.1761-1.19870.18521100.152340X-RAY DIFFRACTION79
1.1987-1.22310.16391070.13462602X-RAY DIFFRACTION86
1.2231-1.24970.15921610.12392664X-RAY DIFFRACTION93
1.2497-1.27880.14051340.1162942X-RAY DIFFRACTION98
1.2788-1.31080.14331540.10182939X-RAY DIFFRACTION100
1.3108-1.34620.15391470.09642964X-RAY DIFFRACTION100
1.3462-1.38580.11071620.09512946X-RAY DIFFRACTION100
1.3858-1.43050.13051770.09132917X-RAY DIFFRACTION100
1.4305-1.48160.12991570.09442938X-RAY DIFFRACTION100
1.4816-1.54090.11961610.09192976X-RAY DIFFRACTION100
1.5409-1.61090.12461550.0952959X-RAY DIFFRACTION100
1.6109-1.69580.11581520.09772979X-RAY DIFFRACTION100
1.6958-1.80190.1361680.1032941X-RAY DIFFRACTION100
1.8019-1.94080.12341620.10592972X-RAY DIFFRACTION100
1.9408-2.13570.13911570.10272962X-RAY DIFFRACTION100
2.1357-2.44390.10681440.11433008X-RAY DIFFRACTION100
2.4439-3.07560.15111790.1342965X-RAY DIFFRACTION100
3.0756-16.28740.14471530.1433074X-RAY DIFFRACTION100

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