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- PDB-1ihg: Bovine Cyclophilin 40, monoclinic form -

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Basic information

Entry
Database: PDB / ID: 1ihg
TitleBovine Cyclophilin 40, monoclinic form
ComponentsCyclophilin 40
KeywordsISOMERASE / PPIASE IMMUNOPHILIN TETRATRICOPEPTIDE
Function / homology
Function and homology information


cellular response to UV-A / lipid droplet organization / cyclosporin A binding / transcription factor binding / positive regulation of viral genome replication / : / Hsp70 protein binding / peptidyl-prolyl cis-trans isomerase activity / nuclear estrogen receptor binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity ...cellular response to UV-A / lipid droplet organization / cyclosporin A binding / transcription factor binding / positive regulation of viral genome replication / : / Hsp70 protein binding / peptidyl-prolyl cis-trans isomerase activity / nuclear estrogen receptor binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / Hsp90 protein binding / protein transport / protein folding / protein-containing complex assembly / positive regulation of apoptotic process / apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat / Cyclophilin-like / Cyclophilin / Tetratricopeptide repeat domain / 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 ...Tetratricopeptide repeat / Cyclophilin-like / Cyclophilin / Tetratricopeptide repeat domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Alpha Horseshoe / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase D
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTaylor, P. / Dornan, J. / Carrello, A. / Minchin, R.F. / Ratajczak, T. / Walkinshaw, M.D.
CitationJournal: Structure / Year: 2001
Title: Two structures of cyclophilin 40: folding and fidelity in the TPR domains.
Authors: Taylor, P. / Dornan, J. / Carrello, A. / Minchin, R.F. / Ratajczak, T. / Walkinshaw, M.D.
History
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclophilin 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7702
Polymers40,6781
Non-polymers921
Water8,809489
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.125, 47.328, 85.563
Angle α, β, γ (deg.)90.00, 119.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cyclophilin 40 / 40 KDA Peptidyl-prolyl cis-trans isomerase


Mass: 40678.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: PET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26882, peptidylprolyl isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 4000, MES Glycerol Sodium Chloride, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 %PEG40001reservoir0.320ml
21 MMES1reservoir0.100ml
350 %(v/v)glycerol1reservoir0.200ml
44 M1reservoir0.1NaCl
610-80 mg/mlprotein1drop
720 mMTris1drop
8100 mM1dropNaCl
5water1reservoir0.280ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1999
RadiationMonochromator: Single Crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→28 Å / Num. all: 41259 / Num. obs: 41259 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.448 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.67
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 9.03 / Num. unique all: 1769 / % possible all: 87.3
Reflection
*PLUS
Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CYCLOPHILIN A

Resolution: 1.8→24 Å / Num. parameters: 13223 / Num. restraintsaints: 11467 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2035 5 %RANDOM
Rwork0.178 ---
all0.178 38413 --
obs0.178 38413 93.5 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3305
Refinement stepCycle: LAST / Resolution: 1.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 6 489 3305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.07
X-RAY DIFFRACTIONs_angle_d0.23

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