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- PDB-1xo7: Crystal structure of cyclophilin from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 1xo7
TitleCrystal structure of cyclophilin from Trypanosoma cruzi
Componentscyclophilin
KeywordsISOMERASE / cyclophilin / rotamase / proline / cis-trans / trypanosoma / cruzi / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM / SGPP
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / 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 speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsCaruthers, J.M. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of cyclophilin from Trypanosoma cruzi
Authors: Caruthers, J.M. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN ANY REFERENCE SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cyclophilin
B: cyclophilin
C: cyclophilin
D: cyclophilin


Theoretical massNumber of molelcules
Total (without water)72,2304
Polymers72,2304
Non-polymers00
Water14,556808
1
A: cyclophilin


Theoretical massNumber of molelcules
Total (without water)18,0581
Polymers18,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cyclophilin


Theoretical massNumber of molelcules
Total (without water)18,0581
Polymers18,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cyclophilin


Theoretical massNumber of molelcules
Total (without water)18,0581
Polymers18,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cyclophilin


Theoretical massNumber of molelcules
Total (without water)18,0581
Polymers18,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.314, 62.142, 64.638
Angle α, β, γ (deg.)109.55, 104.21, 104.92
Int Tables number1
Space group name H-MP1
Detailsputative monomer

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Components

#1: Protein
cyclophilin


Mass: 18057.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-star / References: UniProt: Q4DPB9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Ammonium Phosphate monobasic, Sodium Acetate, PEG8000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 25K, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2004 / Details: custom
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→56.8 Å / Num. all: 80854 / Num. obs: 80854 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rsym value: 0.103 / Net I/σ(I): 7.2
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.55 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ELVESdata reduction
ELVESdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYW.pdb

1dyw


Resolution: 1.61→56.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.492 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.096 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19774 4251 5 %RANDOM
Rwork0.17899 ---
all0.179 80854 --
obs0.18 80854 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20.29 Å20.36 Å2
2--1.11 Å20.14 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.61→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 0 808 5896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0225196
X-RAY DIFFRACTIONr_bond_other_d00.024648
X-RAY DIFFRACTIONr_angle_refined_deg2.611.9397008
X-RAY DIFFRACTIONr_angle_other_deg3.668310860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975660
X-RAY DIFFRACTIONr_chiral_restr0.1890.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025864
X-RAY DIFFRACTIONr_gen_planes_other0.0220.021064
X-RAY DIFFRACTIONr_nbd_refined0.210.2918
X-RAY DIFFRACTIONr_nbd_other0.2970.25140
X-RAY DIFFRACTIONr_nbtor_other0.1230.22492
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2391
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.235
X-RAY DIFFRACTIONr_mcbond_it1.6371.53260
X-RAY DIFFRACTIONr_mcangle_it2.59125264
X-RAY DIFFRACTIONr_scbond_it4.47131936
X-RAY DIFFRACTIONr_scangle_it6.584.51744
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 296
Rwork0.258 5589
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)
10.2766-0.1397-0.15770.2030.11850.11430.0135-0.0065-0.0205-0.0218-0.0402-0.0108-0.01620.00210.02670.0221-0.00330.00230.0520.00740.027551.840827.537415.8955
20.44570.07020.08220.30470.04030.2287-0.014-0.0066-0.0371-0.02320.03950.0085-0.02370.0534-0.02560.0186-0.0010.00260.0285-0.01510.02734.44490.045851.7492
30.1828-0.10440.06520.2109-0.05710.2322-0.0329-0.003-0.01050.03890.02320.0216-0.00290.00530.00970.03150.00520.01030.02230.0040.0335-17.976920.618140.779
40.3678-0.23160.03780.2840.02610.3395-0.0113-0.0129-0.0084-0.04070.00840.0321-0.03830.03070.00290.0341-0.0108-0.00360.0035-0.00020.03533.7856-15.115434.5262
50.0678-0.0333-0.02020.0338-0.03680.01730.0007-0.0072-0.0137-0.0049-0.00080.00710.00390.00410.00010.0485-0.0040.00350.0394-0.0140.038915.93637.980636.4511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 166
2X-RAY DIFFRACTION2B1 - 166
3X-RAY DIFFRACTION3C1 - 166
4X-RAY DIFFRACTION4D1 - 166
5X-RAY DIFFRACTION5A167 - 362
6X-RAY DIFFRACTION5C167 - 366
7X-RAY DIFFRACTION5B167 - 371
8X-RAY DIFFRACTION5D167 - 373

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