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- PDB-3pmp: Crystal Structure of Cyclophilin A from Moniliophthora perniciosa... -

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Basic information

Entry
Database: PDB / ID: 3pmp
TitleCrystal Structure of Cyclophilin A from Moniliophthora perniciosa in complex with Cyclosporin A
Components
  • CYCLOSPORIN A
  • Cyclophilin A
KeywordsISOMERASE/IMMUNOSUPPRESSANT / peptidyl prolyl isomerase / ISOMERASE-IMMUNOSUPPRESSANT complex
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / 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
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesMoniliophthora perniciosa (fungus)
Tolypocladium inflatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsMonzani, P. / Pereira, H.M. / Gramacho, K.P. / Meirelles, F.V. / Oliva, G. / Cascardo, J.C.C.
CitationJournal: To be Published
Title: Crystal Structure of Cyclophilin A from Moniliophthora perniciosa
Authors: Monzani, P. / Pereira, H.M. / Gramacho, K.P. / Meirelles, F.V. / Oliva, G. / Cascardo, J.C.C.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Other
Revision 1.2Jan 28, 2015Group: Other
Revision 1.3May 31, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclophilin A
B: Cyclophilin A
C: CYCLOSPORIN A
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)38,1244
Polymers38,1244
Non-polymers00
Water7,242402
1
A: Cyclophilin A
C: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)19,0622
Polymers19,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-8 kcal/mol
Surface area7780 Å2
MethodPISA
2
B: Cyclophilin A
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)19,0622
Polymers19,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-8 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.028, 104.028, 61.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Cyclophilin A


Mass: 17841.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moniliophthora perniciosa (fungus) / Gene: Cpy / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: E3P6K5*PLUS, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) Tolypocladium inflatum (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 1.8 M ammonium sulfate, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.42
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
ReflectionResolution: 1.47→73.559 Å / Num. obs: 57546 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 14.2
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.66 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
MOLREPphasing
PHENIX1.6_289refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→26.41 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0.04 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 2759 5.07 %
Rwork0.164 --
obs0.165 54370 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.66 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.6326 Å20 Å2-0 Å2
2--1.6326 Å2-0 Å2
3----3.2652 Å2
Refinement stepCycle: LAST / Resolution: 1.47→26.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 0 402 3076
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0692-0.0384-0.01340.7025-0.19470.61740.00720.0167-0.0058-0.01780.03560.04360.0486-0.0779-0.04010.0865-0.01140.00150.10940.00930.09726.5311-7.37218.767
20.23380.13440.04130.67620.04250.3392-0.0104-0.02070.02390.0010.01450.061-0.041-0.0322-0.00560.03980.00930.00270.04660.00420.045427.15678.7951-12.312
30.29310.0483-0.1050.26280.05670.06040.0275-0.0690.00170.0006-0.00030.0350.02080.0155-0.02890.1457-0.0183-0.00410.1040.00740.087830.73925.3643-34.3542
40.03050.0232-0.02190.019-0.00670.1450.00560.00670.01430.02440.01840.06180.00380.0773-0.02630.14950.00910.00910.10060.00810.098430.5097-4.1591-20.456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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