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- PDB-2c3b: The Crystal Structure of Aspergillus fumigatus Cyclophilin reveal... -

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Basic information

Entry
Database: PDB / ID: 2c3b
TitleThe Crystal Structure of Aspergillus fumigatus Cyclophilin reveals 3D Domain Swapping of a Central Element
ComponentsPPIASE
KeywordsISOMERASE / 3D DOMAIN SWAPPING / MISFOLDING / PPIASE / ASP F 11 / ALLERGEN / ROTAMASE
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / identical protein binding / 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 / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsLimacher, A. / Kloer, D.P. / Fluckiger, S. / Folkers, G. / Crameri, R. / Scapozza, L.
CitationJournal: Structure / Year: 2006
Title: The Crystal Structure of Aspergillus Fumigatus Cyclophilin Reveals 3D Domain Swapping of a Central Element
Authors: Limacher, A. / Kloer, D.P. / Fluckiger, S. / Folkers, G. / Crameri, R. / Scapozza, L.
History
DepositionOct 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PPIASE
B: PPIASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9894
Polymers37,7962
Non-polymers1922
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.829, 64.829, 156.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PPIASE / CYCLOPHILIN


Mass: 18898.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q9Y7F6, UniProt: Q4WHY9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.93 Å3/Da / Density % sol: 57.75 %
Crystal growpH: 6
Details: DROP SOLUTION: 13% AMMONIUM SULFATE, 0.1 M MES PH 6. RESERVOIR SOLUTION: 50% AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.85→45.6 Å / Num. obs: 33079 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.2
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→55.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.037 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1675 5.1 %RANDOM
Rwork0.189 ---
obs0.191 31360 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 10 123 2295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222224
X-RAY DIFFRACTIONr_bond_other_d0.0010.022018
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.9442989
X-RAY DIFFRACTIONr_angle_other_deg0.93234704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.095271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84323.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60215398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.021516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined0.1980.2382
X-RAY DIFFRACTIONr_nbd_other0.1780.21928
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21070
X-RAY DIFFRACTIONr_nbtor_other0.0850.21326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.941.51766
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3322216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5293998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1874.5773
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 136
Rwork0.24 2264
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)
14.00141.72920.31433.99541.43012.4284-0.22460.48850.2039-0.690.15880.2555-0.2537-0.12620.0658-0.0108-0.05110.0008-0.14720.0205-0.170724.2957-3.988574.4592
26.44290.24410.08195.98441.59137.2573-0.09370.43420.0639-0.36030.10320.5598-0.1177-0.438-0.0094-0.12770.08140.0171-0.2162-0.0357-0.089520.81096.214695.1479
34.0487-2.0089-0.13963.98110.362.7609-0.2021-0.4112-0.1790.52470.17490.33940.2408-0.08820.0273-0.0380.09410.0591-0.18330.0131-0.140525.18912.1288107.0887
49.04482.8201-0.9565.71694.255813.0616-0.0677-0.13290.05060.1294-0.01270.74590.0744-0.44820.0804-0.1361-0.02460.024-0.2265-0.0346-0.084418.7833-4.492684.2331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 69
2X-RAY DIFFRACTION1A128 - 171
3X-RAY DIFFRACTION2A92 - 127
4X-RAY DIFFRACTION3B1 - 68
5X-RAY DIFFRACTION3B128 - 171
6X-RAY DIFFRACTION4B96 - 127

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