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Yorodumi- PDB-2x32: Structure of a polyisoprenoid binding domain from Saccharophagus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x32 | ||||||
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Title | Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown | ||||||
Components | CELLULOSE-BINDING PROTEIN | ||||||
Keywords | CARBOHYDRATE-BINDING PROTEIN / OXIDOREDUCTION / MARINE BACTERIA / POLYISOPRENOID TRANSPORT | ||||||
Function / homology | Function and homology information polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / membrane Similarity search - Function | ||||||
Biological species | SACCHAROPHAGUS DEGRADANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Vincent, F. / Dal Molin, D. / Weiner, R.M. / Bourne, Y. / Henrissat, B. | ||||||
Citation | Journal: FEBS Lett. / Year: 2010 Title: Structure of a Polyisoprenoid Binding Domain from Saccharophagus Degradans Implicated in Plant Cell Wall Breakdown Authors: Vincent, F. / Dalmolin, D. / Weiner, R.M. / Bourne, Y. / Henrissat, B. | ||||||
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 | 2x32.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x32.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 2x32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x32 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x32 | HTTPS FTP |
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-Related structure data
Related structure data | 2x34SC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.96196, -0.08183, 0.26066), Vector: |
-Components
#1: Protein | Mass: 19326.820 Da / Num. of mol.: 2 / Fragment: YCEI-LIKE DOMAIN, RESIDUES 199-371 Source method: isolated from a genetically manipulated source Details: OCTAPRENYL PYROPHOSPHATE BOUND TO THE PROTEIN / Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS (bacteria) / Strain: 2-40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: Q21LI5 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | N-TERMINAL HISTIDINE TAG | |
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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: 2.23 Å3/Da / Density % sol: 44.9 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: pH 5.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→35 Å / Num. obs: 51047 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X34 Resolution: 1.55→51.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.841 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.379 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→51.23 Å
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Refine LS restraints |
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