+Open data
-Basic information
Entry | Database: PDB / ID: 1oki | ||||||
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Title | Crystal structure of truncated human beta-B1-crystallin | ||||||
Components | BETA CRYSTALLIN B1 | ||||||
Keywords | EYE LENS PROTEIN / CRYSTALLIN / CATARACT | ||||||
Function / homology | Function and homology information structural constituent of eye lens / lens development in camera-type eye / visual perception Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | van Montfort, R.L.M. / Bateman, O.A. / Lubsen, N.H. / Slingsby, C. | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Crystal Structure of Truncated Human Beta-B1-Crystallin Authors: Van Montfort, R.L.M. / Bateman, O.A. / Lubsen, N.H. / Slingsby, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oki.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oki.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1oki ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1oki | HTTPS FTP |
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-Related structure data
Related structure data | 2bb2S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0001, -1, -0.0003), Vector: |
-Components
#1: Protein | Mass: 24252.088 Da / Num. of mol.: 2 / Fragment: CRYSTALLIN DOMAINS, RESIDUES 42-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EYE LENS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53674 #2: Water | ChemComp-HOH / | Compound details | CRYSTALLINS FORM THE DOMINANT STRUCTURAL COMPONENTS OF THE VERTEBRATE EYE LENS. THE PROTEIN EXISTS ...CRYSTALLIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 24-30% PEG4000, 0.1M TRIS/HCL PH 7.0-8.5, 0.2M MGCL2 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: batch method / Details: Bateman, O.A., (2001) Exp. Eye Res., 73, 321. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→35 Å / Num. obs: 60531 / % possible obs: 85.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 8.9 |
Reflection | *PLUS Highest resolution: 1.4 Å / Num. measured all: 315295 / Rmerge(I) obs: 0.043 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BB2 Resolution: 1.4→45.17 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.26 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL DATASET PROCESSED IN P43212. TYR130 AT THE CRYSTALLOGRAPHIC TWOFOLD CLASHED WITH TYR130 OF A SYMMETRY RELATED MOLECULE. AS MOLECULE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL DATASET PROCESSED IN P43212. TYR130 AT THE CRYSTALLOGRAPHIC TWOFOLD CLASHED WITH TYR130 OF A SYMMETRY RELATED MOLECULE. AS MOLECULE IS A DIMER IN SOLULTION, LOWERED SPACE GROUP TO P43 WITH TWOFOLD NCS SYMMETRY. TYR130 POSSIBLY IN TWO CONFORMATIONS. PRIMARY CONFORMATION MODELLED.
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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: 17.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→45.17 Å
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Refine LS restraints |
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