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- PDB-2cmt: The structure of reduced cyclophilin A from s. mansoni -

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Basic information

Entry
Database: PDB / ID: 2cmt
TitleThe structure of reduced cyclophilin A from s. mansoni
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASE E
KeywordsISOMERASE / ROTAMASE ACTIVITY / ROTAMASE / RNA-BINDING / CYCLOSPORIN / CYCLOPHILIN / SCHISTOSOMA / BETA-BARREL
Function / homology
Function and homology information


cyclosporin A binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein folding / mitochondrion / RNA binding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E / 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 / RNA recognition motif ...Peptidyl-prolyl cis-trans isomerase E / 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 / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Peptidyl-prolyl cis-trans isomerase E
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGourlay, L.J. / Angelucci, F. / Bellelli, A. / Boumis, G. / Miele, A.E. / Brunori, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Three-Dimensional Structure of Two Redox States of Cyclophilin a from Schistosoma Mansoni. Evidence for Redox Regulation of Peptidyl-Prolyl Cis-Trans Isomerase Activity.
Authors: Gourlay, L.J. / Angelucci, F. / Baiocco, P. / Boumis, G. / Brunori, M. / Bellelli, A. / Miele, A.E.
History
DepositionMay 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2772
Polymers19,2181
Non-polymers591
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.654, 59.213, 61.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E / CYCLOPHILIN A / PPIASE E / ROTAMASE E / CYCLOPHILIN E


Mass: 19218.100 Da / Num. of mol.: 1 / Fragment: RESIDUES 102-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q26548, peptidylprolyl isomerase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPPIASES TAKES PART IN THE CIS-TRANS ISOMERIZATION OF PROLINE IMIDIC PEPTIDE BONDS IN OLIGOPEPTIDES.

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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: 38.6 %
Crystal growpH: 5.5 / Details: 0.1M IMIDAZOLE/MALATE PH 5.5, 20 % PEG 600

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.5→62.02 Å / Num. obs: 23994 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.21
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 14 % / Rmerge(I) obs: 0.17 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZMF

1zmf


Resolution: 1.5→42.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.12 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1226 5.1 %RANDOM
Rwork0.182 ---
obs0.184 22715 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 4 100 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221338
X-RAY DIFFRACTIONr_bond_other_d0.0010.021201
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9461807
X-RAY DIFFRACTIONr_angle_other_deg0.71332804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9323.23165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.95315233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9021512
X-RAY DIFFRACTIONr_chiral_restr0.0640.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021544
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
X-RAY DIFFRACTIONr_nbd_refined0.1870.2216
X-RAY DIFFRACTIONr_nbd_other0.1670.21210
X-RAY DIFFRACTIONr_nbtor_refined0.170.2669
X-RAY DIFFRACTIONr_nbtor_other0.0770.2802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0730.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4441.51082
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.50621337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8163590
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1494.5462
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 94
Rwork0.191 1636

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