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- PDB-3rfy: Crystal structure of arabidopsis thaliana cyclophilin 38 (ATCYP38) -

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Basic information

Entry
Database: PDB / ID: 3rfy
TitleCrystal structure of arabidopsis thaliana cyclophilin 38 (ATCYP38)
ComponentsPeptidyl-prolyl cis-trans isomerase CYP38, chloroplastic
KeywordsISOMERASE / CYCLOPHILIN / CYP38 / PEPTIDYL PROLYL ISOMERASE / PPIASE / TLP
Function / homology
Function and homology information


thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid lumen / thylakoid / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / defense response to bacterium / cytosol
Similarity search - Function
Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle / PsbQ-like domain superfamily / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.39 Å
AuthorsVasudevan, D. / Swaminathan, K.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal structure of Arabidopsis cyclophilin38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism.
Authors: Vasudevan, D. / Fu, A. / Luan, S. / Swaminathan, K.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Oct 16, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 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 CYP38, chloroplastic


Theoretical massNumber of molelcules
Total (without water)40,4191
Polymers40,4191
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic

A: Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic


Theoretical massNumber of molelcules
Total (without water)80,8372
Polymers80,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3490 Å2
ΔGint-17 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.690, 96.720, 166.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic / PPIase CYP38 / Rotamase CYP38 / Thylakoid lumen PPIase


Mass: 40418.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g01480, CYP38, F4P13.3 / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9SSA5, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 20% PEG 6000, 2.5% T-BUTANOL, 100MM SODIUM CITRATE (PH 5.5), VAPOR BATCH, TEMPERATURE 293K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9797, 0.9794, 0.9500
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2006 / Details: VERTICALLY COLLIMATING MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97941
30.951
ReflectionResolution: 2.39→50 Å / Num. obs: 19441 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 43.4 Å2 / Rsym value: 0.067 / Net I/σ(I): 19.21
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.23 / % possible all: 91.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.39→19.89 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3188772.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 669 4.9 %RANDOM
Rwork0.248 ---
obs0.248 16411 86.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.63 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 69.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.49 Å20 Å20 Å2
2---3.78 Å20 Å2
3----2.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.39→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 0 114 2879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.161.5
X-RAY DIFFRACTIONc_mcangle_it3.682
X-RAY DIFFRACTIONc_scbond_it4.052
X-RAY DIFFRACTIONc_scangle_it5.242.5
LS refinement shellResolution: 2.39→2.54 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 90 5.2 %
Rwork0.344 1642 -
obs--55.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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