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- PDB-1a33: PEPTIDYLPROLYL ISOMERASE, CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI -

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Basic information

Entry
Database: PDB / ID: 1a33
TitlePEPTIDYLPROLYL ISOMERASE, CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI
ComponentsPEPTIDYLPROLYL ISOMERASE
KeywordsISOMERASE / PEPTIDYL-PROLYL CIS-TRANS / PEPTIDYLPROLYL ISOMERASE
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / mitochondrion
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMikol, V. / Ma, D. / Carlow, C.K.S.
CitationJournal: Protein Sci. / Year: 1998
Title: Crystal structure of the cyclophilin-like domain from the parasitic nematode Brugia malayi.
Authors: Mikol, V. / Ma, D. / Carlow, C.K.
History
DepositionJan 27, 1998Processing site: BNL
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYLPROLYL ISOMERASE


Theoretical massNumber of molelcules
Total (without water)19,5041
Polymers19,5041
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.900, 57.900, 140.130
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 PEPTIDYLPROLYL ISOMERASE


Mass: 19504.418 Da / Num. of mol.: 1 / Fragment: CYCLOPHILIN-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: BMCYP-1 / Plasmid: PMAL-C2 / Gene (production host): MBP FUSION PROTEIN / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267 / References: UniProt: Q27450, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.67 Å3/Da / Density % sol: 54.1 %
Crystal growpH: 6
Details: THE INITIAL 6 UL DROP CONSISTED OF 50 MM MES-NAOH PH 6.0, 0.9 M (NH4)2SO4, 1MM PROTEIN. THE 1 ML RESERVOIR SOLUTION CONSISTED OF 100 MM MES-NAOH PH 6.0, 1.8 M (NH4)2SO4
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
2100 mMMES-NaOH1reservoir
31.8 Mammonium sulfate1reservoir
450 mMMES-NaOH1drop
50.9 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→10 Å / Num. obs: 13361 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 36
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 22 / Rsym value: 0.08 / % possible all: 96
Reflection
*PLUS
Num. measured all: 84704
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWA

1cwa


Resolution: 2.15→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 677 5 %RANDOM
Rwork0.169 ---
obs0.169 13236 97.7 %-
Displacement parametersBiso mean: 12 Å2
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 234 1572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.75
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.15→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.17 76 5 %
Rwork0.201 1520 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.75
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45

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