+Open data
-Basic information
Entry | Database: PDB / ID: 1us3 | ||||||
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Title | Native xylanase10C from Cellvibrio japonicus | ||||||
Components | ENDO-BETA-1,4-XYLANASE PRECURSOR | ||||||
Keywords | HYDROLASE / CARBOHYDRATE BINDING MODULE / XYLAN DEGRADATION | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cell outer membrane Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Pell, G. / Szabo, L. / Charnock, S.J. / Xie, H. / Gloster, T.M. / Davies, G.J. / Gilbert, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural and Biochemical Analysis of Cellvibrio Japonicus Xylanase 10C: How Variation in Substrate-Binding Cleft Influences the Catalytic Profile of Family Gh-10 Xylanases Authors: Pell, G. / Szabo, L. / Charnock, S.J. / Xie, H. / Gloster, T.M. / Davies, G.J. / Gilbert, H.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1us3.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1us3.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 1us3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1us3_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 1us3_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 1us3_validation.xml.gz | 26 KB | Display | |
Data in CIF | 1us3_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/1us3 ftp://data.pdbj.org/pub/pdb/validation_reports/us/1us3 | HTTPS FTP |
-Related structure data
Related structure data | 1us2C 1clxS C: citing same article (ref.) 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: 58210.430 Da / Num. of mol.: 1 Fragment: CARBOHYDRATE BINDING MODULE AND CATALYTIC MODULE, RESIDUES (86-606) Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER\:PLYSS / References: UniProt: Q59675, endo-1,4-beta-xylanase | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | ChemComp-TRS / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | NUMBERING IS CONSISTENT WITH THE SWISSPROT ENTRY FOR THE GENE. 3 MISTAKES WERE DISCOVERED IN ...NUMBERING IS CONSISTENT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.9 % | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: 30 MG/ML PROTEIN 0.2 M SODIUM IODIDE, 20% PEG 3350, pH 7.00 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
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: ID14-4 / Wavelength: 0.932 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) OR SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 52228 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.6 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 20 Å / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 98 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CLX Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.258 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ATOMS THAT COULD NOT BE PLACED RELIABLY IN ELECTRON DENSITY HAVE BEEN SET TO ZERO OCCUPANCY
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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: 17.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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