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- PDB-4eyv: Crystal structure of Cyclophilin A like protein from Piriformospo... -

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Basic information

Entry
Database: PDB / ID: 4eyv
TitleCrystal structure of Cyclophilin A like protein from Piriformospora indica
ComponentsPeptidyl-prolyl cis-trans isomeraseProlyl isomerase
KeywordsISOMERASE / Cyclophilin motif / Fungus / salt tolerance
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
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
: / PHOSPHATE ION / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesPiriformospora indica (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBhatt, H. / Pal, R.K. / Tuteja, N. / Bhavesh, N.S.
CitationJournal: Sci Rep / Year: 2013
Title: Structure of RNA-interacting Cyclophilin A-like protein from Piriformospora indica that provides salinity-stress tolerance in plants
Authors: Trivedi, D.K. / Bhatt, H. / Pal, R.K. / Tuteja, R. / Garg, B. / Johri, A.K. / Bhavesh, N.S. / Tuteja, N.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Structure summary
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,90618
Polymers54,4243
Non-polymers48115
Water9,404522
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2736
Polymers18,1411
Non-polymers1315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3687
Polymers18,1411
Non-polymers2266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2665
Polymers18,1411
Non-polymers1244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.252, 144.108, 110.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-422-

HOH

21B-460-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 2 / Auth seq-ID: 6 - 162 / Label seq-ID: 9 - 165

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase


Mass: 18141.471 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piriformospora indica (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: C6KGV3, peptidylprolyl isomerase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 4.44 Å3/Da / Density % sol: 72.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 11, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→27.03 Å / Num. obs: 68106

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoBuildphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3k0n

3k0n


Resolution: 1.97→27.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1854 / WRfactor Rwork: 0.162 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8843 / SU B: 2.229 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0982 / SU Rfree: 0.0961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 3444 5.1 %RANDOM
Rwork0.1588 ---
obs0.1601 68106 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.37 Å2 / Biso mean: 29.5402 Å2 / Biso min: 18.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--1.93 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.97→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 19 522 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0223989
X-RAY DIFFRACTIONr_angle_refined_deg2.2821.9355427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03925.027187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90415688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6741515
X-RAY DIFFRACTIONr_chiral_restr0.2040.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213074
X-RAY DIFFRACTIONr_mcbond_it1.3731.52466
X-RAY DIFFRACTIONr_mcangle_it2.21324012
X-RAY DIFFRACTIONr_scbond_it3.52931523
X-RAY DIFFRACTIONr_scangle_it5.864.51390
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A615TIGHT POSITIONAL0.060.05
2B615TIGHT POSITIONAL0.080.05
3C615TIGHT POSITIONAL0.050.05
1A524MEDIUM POSITIONAL0.10.5
2B524MEDIUM POSITIONAL0.110.5
3C524MEDIUM POSITIONAL0.140.5
1A615TIGHT THERMAL0.640.5
2B615TIGHT THERMAL0.850.5
3C615TIGHT THERMAL1.070.5
1A524MEDIUM THERMAL0.532
2B524MEDIUM THERMAL0.672
3C524MEDIUM THERMAL0.782
LS refinement shellResolution: 1.972→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 244 -
Rwork0.23 4729 -
all-4973 -
obs--99.58 %

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