+Open data
-Basic information
Entry | Database: PDB / ID: 5ht1 | ||||||
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Title | Structure of apo C. glabrata FKBP12 | ||||||
Components | FK506-binding protein 1 | ||||||
Keywords | ISOMERASE / FKBP12 / C. glabrata / pahtogenesis | ||||||
Function / homology | Function and homology information regulation of homoserine biosynthetic process / macrolide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / chromatin organization / cytoplasm Similarity search - Function | ||||||
Biological species | Candida glabrata (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.651 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Mbio / Year: 2016 Title: Structures of Pathogenic Fungal FKBP12s Reveal Possible Self-Catalysis Function. Authors: Tonthat, N.K. / Juvvadi, P.R. / Zhang, H. / Lee, S.C. / Venters, R. / Spicer, L. / Steinbach, W.J. / Heitman, J. / Schumacher, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ht1.cif.gz | 33.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ht1.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ht1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/5ht1 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/5ht1 | HTTPS FTP |
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-Related structure data
Related structure data | 5htgC 5huaC 5hw6C 5hw7C 5hw8C 5hwbC 5hwcC 5i98C 5j6eC C: citing same article (ref.) |
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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: 12240.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus) Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65 Gene: FPR1, CAGL0K09724g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FMA3, 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: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, 0.1 M Tris 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→43.508 Å / Num. obs: 3991 / % possible obs: 99.99 % / Redundancy: 3.3 % / Net I/σ(I): 11.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.651→43.508 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.584 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.651→43.508 Å
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Refine LS restraints |
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LS refinement shell |
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