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Yorodumi- PDB-1oh4: Structural and thermodynamic dissection of specific mannan recogn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oh4 | |||||||||
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Title | Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module | |||||||||
Components | BETA-MANNOSIDASE | |||||||||
Keywords | HYDROLASE / CARBOHYDRATE BINDING MODULE / MANNAN / LECTIN / GLYCOSIDE HYDROLASE | |||||||||
Function / homology | Function and homology information mannan endo-1,4-beta-mannosidase activity / metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Boraston, A.B. / Revett, T.J. / Boraston, C.M. / Nurizzo, D. / Davies, G.J. | |||||||||
Citation | Journal: Structure / Year: 2003 Title: Structural and Thermodynamic Dissection of Specific Mannan Recognition by a Carbohydrate Binding Module, Tmcbm27 Authors: Boraston, A.B. / Revett, T.J. / Boraston, C.M. / Nurizzo, D. / Davies, G.J. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oh4.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oh4.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 1oh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oh4_validation.pdf.gz | 752.4 KB | Display | wwPDB validaton report |
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Full document | 1oh4_full_validation.pdf.gz | 755.2 KB | Display | |
Data in XML | 1oh4_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1oh4_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1oh4 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1oh4 | HTTPS FTP |
-Related structure data
Related structure data | 1of3SC 1of4C S: Starting model for refinement 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 20489.016 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 505-680 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Plasmid: PET 28 TMCBM27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RIK9 |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-[alpha-D-galactopyranose-(1-6)]beta-D-mannopyranose-(1-4)-[alpha-D- ...beta-D-mannopyranose-(1-4)-[alpha-D-galactopyranose-(1-6)]beta-D-mannopyranose-(1-4)-[alpha-D-galactopyranose-(1-6)]beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 186 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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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: 1.83 Å3/Da / Density % sol: 32 % |
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Crystal grow | pH: 4.6 Details: 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→1.42 Å / Num. obs: 31455 / % possible obs: 97.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.9 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OF3 Resolution: 1.35→48.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.721 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.055 / 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: 11.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→48.22 Å
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Refine LS restraints |
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