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- PDB-1e3b: CYCLOPHILIN 3 FROM C.ELEGANS COMPLEXED WITH AUP(ET)3 -

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Basic information

Entry
Database: PDB / ID: 1e3b
TitleCYCLOPHILIN 3 FROM C.ELEGANS COMPLEXED WITH AUP(ET)3
ComponentsCYCLOPHILIN 3
KeywordsISOMERASE / AUPET3 ADDUCT CYCLOPHILIN ANTIARTHRITIC GOLD
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
TRIETHYLPHOSPHANE / : / Peptidyl-prolyl cis-trans isomerase 3
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZou, J. / Taylor, P. / Dornan, J. / Robinson, S.P. / Walkinshaw, M.D. / Sadler, P.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2000
Title: First Crystal Structure of a Medicinally Relevant Gold Protein Complex:Unexpected Binding of [Au(Pet (3))](+) to Histidine
Authors: Zou, J. / Taylor, P. / Dornan, J. / Robinson, S.P. / Walkinshaw, M.D. / Sadler, P.J.
History
DepositionJun 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5May 1, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CYCLOPHILIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8913
Polymers18,5761
Non-polymers3152
Water3,909217
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.157, 61.157, 123.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CYCLOPHILIN 3


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) / Strain (production host): BL21 / References: UniProt: P52011
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#3: Chemical ChemComp-3EP / TRIETHYLPHOSPHANE


Mass: 118.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.63 Å3/Da / Density % sol: 60.29 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP PH5.6 15.5% W/V MPEG 5000, 50 MM SODIUM CITRATE. WELL SOLUTION: 31% MPEG 5000, 100MM SODIUM CITRATE, pH 5.60
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
250 mMsodium citrate1drop
316-17.5 %(w/v)mPEG50001drop
4100 mMsodium citrate1reservoir
532-35 %(w/v)mPEG50001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.3
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 17, 1999 / Details: PT COATED TORROIDAL MIRRO
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. obs: 20154 / % possible obs: 98.3 % / Redundancy: 4.12 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.03
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 9.92 / % possible all: 1
Reflection
*PLUS
Num. measured all: 185907
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CYCLOPHILIN 3 NATIVE

Resolution: 1.85→31 Å / Num. parameters: 6117 / Num. restraintsaints: 5315 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: AU PET3 PARAMETERS CALCULATED FROM SMALL MOLECULE DATABASE (CCDC)
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1001 0.1 %RANDOM
all0.1848 19153 --
obs0.1848 -93.4 %-
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: 1526
Refinement stepCycle: LAST / Resolution: 1.85→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 8 217 1521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0276
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.036

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