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- PDB-1a58: CYCLOPHILIN FROM BRUGIA MALAYI -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1a58
TitleCYCLOPHILIN FROM BRUGIA MALAYI
ComponentsCYCLOPHILIN
KeywordsISOMERASE / PPIASE
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / plasma membrane / cytosol
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 1
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsTaylor, P. / Page, A.P. / Kontopidis, G. / Husi, H. / Walkinshaw, M.D.
CitationJournal: FEBS Lett. / Year: 1998
Title: The X-ray structure of a divergent cyclophilin from the nematode parasite Brugia malayi.
Authors: Taylor, P. / Page, A.P. / Kontopidis, G. / Husi, H. / Walkinshaw, M.D.
History
DepositionFeb 20, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLOPHILIN


Theoretical massNumber of molelcules
Total (without water)19,5041
Polymers19,5041
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.215, 58.215, 141.944
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


Mass: 19504.418 Da / Num. of mol.: 1 / Fragment: CYCLOPHILIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: CYCLOPHILIN / Plasmid: PMAL-C2 / Gene (production host): CYCLOPHILIN / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 BLUE SUPERCOMPETANT / References: UniProt: Q27450
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growpH: 6.5
Details: 50MM IMIDAZOLE AT PH6.5, 15% SAT. AMMONIUM SULFATE 0.02% SODIUM AZIDE, 0.56 MM PROTEIN CONC.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMimidazole1drop
215 %satammonium sulfate1drop
30.02 %(w/v)1dropNaN3
40.56 mMbmCyp-11drop
5100 mMimidazole1reservoir
630 %satammonium sulfate1reservoir
70.02 %(w/v)1reservoirNaN3

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 26.85 Å2
Reflection
*PLUS
Highest resolution: 1.95 Å / Num. obs: 18055 / % possible obs: 96.9 % / Num. measured all: 103228 / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementResolution: 1.95→24 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: SHELX97 WAS USED INITIALLY WITH SAME CROSS-VALIDATION DATA
RfactorNum. reflection% reflectionSelection details
Rfree0.233 881 5 %RANDOM
Rwork0.199 ---
obs0.199 17458 93.5 %-
Displacement parametersBiso mean: 27.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 0 155 1520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.426
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.01
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.358
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.91.5
X-RAY DIFFRACTIONx_mcangle_it5.12
X-RAY DIFFRACTIONx_scbond_it3.82
X-RAY DIFFRACTIONx_scangle_it6.62.5
LS refinement shellResolution: 1.95→2.04 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.309 97 5 %
Rwork0.288 1936 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Version: 3.851 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.02
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.358
LS refinement shell
*PLUS
Rfactor obs: 0.288

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