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- PDB-1iip: Bovine Cyclophilin 40, Tetragonal Form -

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Basic information

Entry
Database: PDB / ID: 1iip
TitleBovine Cyclophilin 40, Tetragonal 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 / nuclear estrogen receptor binding / positive regulation of protein secretion / peptidylprolyl isomerase ...cellular response to UV-A / lipid droplet organization / cyclosporin A binding / transcription factor binding / positive regulation of viral genome replication / : / Hsp70 protein binding / nuclear estrogen receptor binding / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Hsp90 protein binding / protein folding / protein transport / protein-containing complex assembly / cilium / positive regulation of apoptotic process / apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA polymerase; domain 1 - #160 / Tetratricopeptide repeat / 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 ...DNA polymerase; domain 1 - #160 / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / DNA polymerase; domain 1 / Tetratricopeptide-like helical domain superfamily / Beta Barrel / Orthogonal Bundle / 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: 2 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 24, 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: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / 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 1.4Nov 6, 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: Cyclophilin 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7702
Polymers40,6781
Non-polymers921
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cyclophilin 40
hetero molecules

A: Cyclophilin 40
hetero molecules

A: Cyclophilin 40
hetero molecules

A: Cyclophilin 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0828
Polymers162,7134
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation5_755-x+2,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area11040 Å2
ΔGint-116 kcal/mol
Surface area50040 Å2
MethodPISA
3
A: Cyclophilin 40
hetero molecules

A: Cyclophilin 40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5414
Polymers81,3572
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)94.585, 94.585, 118.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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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 / Production host: Escherichia coli (E. coli) / 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.: 212 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, Imidazole glycerol Tris Sodium Chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
21 Mimidazole1reservoir0.100ml
350 %(v/v)glycerol1reservoir0.140ml
510-80 mg/mlprotein1drop
620 mMTris1drop
7100 mM1dropNaCl
1MPD1reservoir0.480ml
4water1reservoir0.280ml

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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 9, 1999
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. all: 37488 / Num. obs: 37488 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.62 % / Biso Wilson estimate: 26.554 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.65
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.15 / % possible all: 90.5
Reflection
*PLUS
Num. obs: 33904

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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: 2→24 Å / Num. parameters: 9975 / Num. restraintsaints: 9240 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1709 5 %RANDOM
Rwork0.236 ---
all0.236 32191 --
obs0.236 32191 87.1 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2493
Refinement stepCycle: LAST / Resolution: 2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 6 212 2493
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_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.09
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_d0.06
X-RAY DIFFRACTIONs_angle_d0.22

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