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- PDB-4e1q: Crystal structure of Wheat Cyclophilin A at 1.25 A resolution -

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Basic information

Entry
Database: PDB / ID: 4e1q
TitleCrystal structure of Wheat Cyclophilin A at 1.25 A resolution
ComponentsPeptidyl-prolyl cis-trans isomeraseProlyl isomerase
KeywordsISOMERASE
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 speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 Å
AuthorsSekhon, S.S. / Jeong, D.G. / Woo, E.J. / Singh, P. / Yoon, T.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural and biochemical characterization of the cytosolic wheat cyclophilin TaCypA-1
Authors: Sekhon, S.S. / Kaur, H. / Dutta, T. / Singh, K. / Kumari, S. / Kang, S. / Park, S.G. / Park, B.C. / Jeong, D.G. / Pareek, A. / Woo, E.J. / Singh, P. / Yoon, T.S.
History
DepositionMar 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)22,2451
Polymers22,2451
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.135, 52.942, 77.767
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 / Prolyl isomerase / Cyclophilin A


Mass: 22245.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: CyP3, CyP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93W25, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.72 Å3/Da / Density % sol: 28.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0M ammonium phosphate dibasic, 0.1M imidazole pH8.0, 0.2M NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.251→26.855 Å / Num. all: 42959 / Num. obs: 42895 / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.251→26.855 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2166 5.05 %RANDOM
Rwork0.1775 ---
all0.1778 42895 --
obs0.1778 42895 99.46 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.593 Å2 / ksol: 0.457 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1542 Å20 Å2-0 Å2
2--2.0553 Å2-0 Å2
3----1.9011 Å2
Refinement stepCycle: LAST / Resolution: 1.251→26.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 0 170 1450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051308
X-RAY DIFFRACTIONf_angle_d1.1051761
X-RAY DIFFRACTIONf_dihedral_angle_d11.651477
X-RAY DIFFRACTIONf_chiral_restr0.075186
X-RAY DIFFRACTIONf_plane_restr0.005234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2508-1.27990.20521390.1889268299
1.2799-1.31190.19381450.18092661100
1.3119-1.34740.16171390.17332711100
1.3474-1.3870.23231570.17942657100
1.387-1.43180.20571400.17692713100
1.4318-1.4830.17331490.16622682100
1.483-1.54230.19681590.17172692100
1.5423-1.61250.18671310.16512703100
1.6125-1.69750.17411480.16592714100
1.6975-1.80390.16661360.16722704100
1.8039-1.94310.19241520.1672731100
1.9431-2.13860.17131400.16822735100
2.1386-2.44790.20541300.17442776100
2.4479-3.08330.17351420.19132814100
3.0833-26.86150.18331590.1857275495

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