+Open data
-Basic information
Entry | Database: PDB / ID: 3b7x | ||||||
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Title | Crystal structure of human FK506-Binding Protein 6 | ||||||
Components | FK506-binding protein 6 | ||||||
Keywords | ISOMERASE / Rotamase / TPR repeat / Williams-Beuren syndrome / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information : / piRNA processing / synaptonemal complex / regulatory ncRNA-mediated gene silencing / FK506 binding / PIWI-interacting RNA (piRNA) biogenesis / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / Meiotic synapsis / meiotic cell cycle ...: / piRNA processing / synaptonemal complex / regulatory ncRNA-mediated gene silencing / FK506 binding / PIWI-interacting RNA (piRNA) biogenesis / positive regulation of viral genome replication / protein peptidyl-prolyl isomerization / Meiotic synapsis / meiotic cell cycle / Hsp90 protein binding / protein folding / spermatogenesis / cell differentiation / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Walker, J.R. / Davis, T. / Butler-Cole, C. / Paramanathan, R. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Human FK506-Binding Protein 6. Authors: Walker, J.R. / Davis, T. / Butler-Cole, C. / Paramanathan, R. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b7x.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b7x.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7x ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7x | HTTPS FTP |
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-Related structure data
Related structure data | 1kt0S 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: 15074.242 Da / Num. of mol.: 1 / Fragment: PPIase FKBP-Type Domain: Residues 12-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP6, FKBP36 / Plasmid: p28a-mhl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75344, 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: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Mixed equal volumes of 1.6M MgSO4, 0.1M MES pH 6.5, and 10 mg/mL protein. Crystals were cryoprotected by transferring the crystals to a drop containing mother liquor to which glycerol was ...Details: Mixed equal volumes of 1.6M MgSO4, 0.1M MES pH 6.5, and 10 mg/mL protein. Crystals were cryoprotected by transferring the crystals to a drop containing mother liquor to which glycerol was added to a final concentration of 20%, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2007 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 10831 / Num. obs: 10831 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rsym value: 0.054 / Net I/σ(I): 46.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 1037 / Rsym value: 0.365 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KT0 Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.637 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.575 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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