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- PDB-1dyw: Biochemical and structural characterization of a divergent loop c... -

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Basic information

Entry
Database: PDB / ID: 1dyw
TitleBiochemical and structural characterization of a divergent loop cyclophilin from Caenorhabditis elegans
ComponentsCYCLOPHILIN 3
KeywordsISOMERASE(PEPTIDYL-PROLYL CIS-TRANS) / ISOMERASE / ROTAMASE
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / mitochondrion / nucleus / 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 3
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDornan, J. / Page, A.P. / Taylor, P. / Wu, S.Y. / Winter, A.D. / Husi, H. / Walkinshaw, M.D.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Biochemical and Structural Characterization of a Divergent Loop Cyclophilin from Caenorhabditis Elegans
Authors: Dornan, J. / Page, A.P. / Taylor, P. / Wu, S.Y. / Winter, A.D. / Husi, H. / Walkinshaw, M.D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: X-Ray Structure of a Monomeric Cyclophilin
Authors: Mikol, V. / Kallen, J. / Pfluegl, G. / Walkinshaw, M.D.
History
DepositionFeb 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 5, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_source ...atom_site / diffrn_source / pdbx_distant_solvent_atoms / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _diffrn_source.type / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_range.sheet_id
Revision 2.1May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.2Dec 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLOPHILIN 3


Theoretical massNumber of molelcules
Total (without water)18,5761
Polymers18,5761
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.608, 60.608, 123.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein CYCLOPHILIN 3 / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3 / PPIASE / ROTAMASE


Mass: 18576.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52011, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.05 Å3/Da / Density % sol: 59.32 %
Crystal growpH: 5.6 / Details: MPEG5000, SODIUM CITRATE, PH 5.6
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
250 mMsodium citrate1drop
315.5 %(w/v)mPEG50001drop
4100 mMsodium citrate1reservoir
531 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 21337 / % possible obs: 97 % / Redundancy: 6.59 % / Rsym value: 0.083 / Net I/σ(I): 11.75
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.587 / Rsym value: 0.278 / % possible all: 96.2
Reflection
*PLUS
Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.278

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CWA

1cwa


Resolution: 1.8→15 Å / Num. parameters: 6247 / Num. restraintsaints: 5295 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 1064 5 %RANDOM
obs0.2152 -97 %-
all-20135 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1561
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 0 252 1548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.37 Å2

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