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Yorodumi- PDB-1a33: PEPTIDYLPROLYL ISOMERASE, CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a33 | ||||||
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Title | PEPTIDYLPROLYL ISOMERASE, CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI | ||||||
Components | PEPTIDYLPROLYL ISOMERASE | ||||||
Keywords | ISOMERASE / PEPTIDYL-PROLYL CIS-TRANS / PEPTIDYLPROLYL ISOMERASE | ||||||
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 | ||||||
Biological species | Brugia malayi (agent of lymphatic filariasis) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Mikol, V. / Ma, D. / Carlow, C.K.S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a33.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a33.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a33 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a33 | HTTPS FTP |
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-Related structure data
Related structure data | 1cwaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.1 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CWA Resolution: 2.15→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGOUT / σ(F): 0
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Displacement parameters | Biso mean: 12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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