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- PDB-3o7t: Crystal Structure of Cyclophilin A from Moniliophthora perniciosa -

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Basic information

Entry
Database: PDB / ID: 3o7t
TitleCrystal Structure of Cyclophilin A from Moniliophthora perniciosa
ComponentsCyclophilin A
KeywordsISOMERASE / Cyclophilin / peptidyl-prolyl cis-trans isomerase
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
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
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesMoniliophthora perniciosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsMonzani, P.S. / Pereira, H.M. / Gramacho, K.P. / Meirelles, F.V. / Oliva, G. / Cascardo, J.C.M.
CitationJournal: To be Published
Title: Crystal Structures of apo-cyclophilin and bounded cyclosporine A from Moniliophthora perniciosa
Authors: Monzani, P.S. / Pereira, H.M. / Gramacho, K.P. / Meirelles, F.V. / Oliva, G. / Cascardo, J.C.M.
History
DepositionJul 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Cyclophilin A


Theoretical massNumber of molelcules
Total (without water)17,9241
Polymers17,9241
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.854, 98.206, 111.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-168-

HOH

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Components

#1: Protein Cyclophilin A


Mass: 17924.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moniliophthora perniciosa (fungus) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: E3P6K5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 30% PEG 400, 100mM Caps pH 10.5., 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: 1.43 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 1.85→73.749 Å / Num. all: 18133 / Num. obs: 18133 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.954.10.5681.31068725820.56898.9
1.95-2.074.20.3931.91023224650.39399
2.07-2.214.20.3042.4964923090.30499.3
2.21-2.394.20.2432.9917021770.24399.7
2.39-2.624.20.1993.7846219930.19999.8
2.62-2.934.30.1584.5785318470.15899.8
2.93-3.384.20.1255.5686016210.12599.9
3.38-4.144.20.0867.7576413870.08699.8
4.14-5.854.20.0668.6460911090.066100
5.85-49.0883.90.05411.125116430.05499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→36.874 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / σ(F): 0.01 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 868 5.08 %Ramdom
Rwork0.1655 ---
obs0.1675 17081 93.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 75.75 Å2 / Biso mean: 17.3438 Å2 / Biso min: 3.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.6852 Å20 Å2-0 Å2
2--6.4375 Å2-0 Å2
3----2.7496 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1263 0 0 178 1441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111301
X-RAY DIFFRACTIONf_angle_d1.2541754
X-RAY DIFFRACTIONf_chiral_restr0.088189
X-RAY DIFFRACTIONf_plane_restr0.005229
X-RAY DIFFRACTIONf_dihedral_angle_d15.217468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.9660.24911370.21542464260187
1.966-2.11780.24051330.17472566269990
2.1178-2.33090.18181410.15272655279693
2.3309-2.66810.20671630.14582713287695
2.6681-3.36120.18641320.14952831296397
3.3612-36.88180.20181620.17182984314698

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