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Yorodumi- PDB-2xhj: Circular permutation provides an evolutionary link between two fa... -
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-Basic information
Entry | Database: PDB / ID: 2xhj | ||||||
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Title | Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules. SeMet form of vCBM60. | ||||||
Components | CALCIUM-DEPENDENT CARBOHYDRATE BINDING MODULE | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / XYLAN / CELLULOSE / GALACTAN / BETA GLUCAN | ||||||
Function / homology | Lipoxygenase-1 - #40 / Lipoxygenase-1 / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å | ||||||
Authors | Montanier, C. / Flint, J.E. / Bolam, D.N. / Xie, H. / Liu, Z. / Rogowski, A. / Weiner, D. / Ratnaparkhe, S. / Nurizzo, D. / Roberts, S.M. ...Montanier, C. / Flint, J.E. / Bolam, D.N. / Xie, H. / Liu, Z. / Rogowski, A. / Weiner, D. / Ratnaparkhe, S. / Nurizzo, D. / Roberts, S.M. / Turkenburg, J.P. / Davies, G.J. / Gilbert, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Circular Permutation Provides an Evolutionary Link between Two Families of Calcium-Dependent Carbohydrate Binding Modules Authors: Montanier, C. / Flint, J.E. / Bolam, D.N. / Xie, H. / Liu, Z. / Rogowski, A. / Weiner, D. / Ratnaparkhe, S. / Nurizzo, D. / Roberts, S.M. / Turkenburg, J.P. / Davies, G.J. / Gilbert, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xhj.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xhj.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xhj_validation.pdf.gz | 412 KB | Display | wwPDB validaton report |
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Full document | 2xhj_full_validation.pdf.gz | 411.9 KB | Display | |
Data in XML | 2xhj_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 2xhj_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/2xhj ftp://data.pdbj.org/pub/pdb/validation_reports/xh/2xhj | HTTPS FTP |
-Related 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: 12931.747 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SELENOMETHIONINE FORM OF THE PROTEIN USED FOR PHASING Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: NCIMB 10462 / Description: NCIMB CULTURE COLLECTION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (NOVAGEN) |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Sequence details | CURRENTLY NO UNIPROT REFERENCE EXISTS FOR ENTRY. ISOLATED GENE IS GENBANK REF: FN908918 AND THE ...CURRENTLY NO UNIPROT REFERENCE EXISTS FOR ENTRY. ISOLATED GENE IS GENBANK REF: FN908918 AND THE EXPRESSED PROTEIN SEQUENCE IS GENBANK REF: CBM95521.1 TITLE: CARBOHYDRA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % Description: THIS IS THE SEMET CRYSTAL FORM USED TO SOLVE THE NATIVE. |
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Crystal grow | Temperature: 293 K / pH: 6 Details: CRYSTALS WERE GROWN AT 4 DEGREES C OR 20 DEGREES C IN 2.1M NA MALATE PH 5.5-6.0 AT A 1:1 OR 3:2 RATIO OF PROTEIN TO MOTHER LIQUOR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→34.1 Å / Num. obs: 11819 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 12.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.73→41.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.277 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.116 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.124 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→41.81 Å
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