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- PDB-1h0p: Cyclophilin_5 from C. elegans -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1h0p
TitleCyclophilin_5 from C. elegans
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASE 5
KeywordsISOMERASE / ROTAMASE
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Peptidyl-prolyl cis-trans isomerase 5
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPicken, N.C. / Eschenlauer, S. / Taylor, P. / Page, A.P. / Walkinshaw, M.D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural and Biological Characterisation of the Gut-Associated Cyclophilin B Isoforms from Caenorhabditis Elegans
Authors: Picken, N.C. / Eschenlauer, S. / Taylor, P. / Page, A.P. / Walkinshaw, M.D.
History
DepositionJun 26, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0452
Polymers19,8911
Non-polymers1541
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.115, 94.115, 41.239
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 5 / PPIASE / ROTAMASE / CYCLOPHILIN-5


Mass: 19890.775 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-204 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52013, peptidylprolyl isomerase
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.4 Å3/Da / Density % sol: 47.9 %
Crystal growpH: 6 / Details: PH 6.0, PEG 4000, LITHIUM CHLORIDE
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110.2 mg/mlprotein1drop
250 mMTris1drop
3300 mM1dropNaCl
45 mg/mldithiothreitol1drop
5100 mMsodium citrate1reservoirpH6.0
634 %(w/v)PEG40001reservoir
720-40 mM1reservoirLiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.75→24 Å / Num. obs: 21525 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 27.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 23.5 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8K

1e8k


Resolution: 1.75→10 Å / Num. parameters: 6488 / Num. restraintsaints: 5794 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1087 5.4 %RANDOM
all0.18 21525 --
obs0.182 -94.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 2 / Occupancy sum non hydrogen: 1608.3
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 8 201 1611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0271
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.069
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 23.5 Å / % reflection Rfree: 5 % / Rfactor all: 0.18 / Rfactor obs: 0.236 / Rfactor Rfree: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.0271
X-RAY DIFFRACTIONs_chiral_restr0.035

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