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Yorodumi- PDB-1odz: Expansion of the glycosynthase repertoire to produce defined mann... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1odz | |||||||||
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Title | Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides | |||||||||
Components | Mannan endo-1,4-beta-mannosidase | |||||||||
Keywords | HYDROLASE / MANNANASE / FAMILY 26 / GLYCOSIDE-HYDROLASE / GLYCOSYNTHASE / MANNO-OLIGOSACCHARIDE | |||||||||
Function / homology | Function and homology information glucomannan metabolic process / galactomannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Cellvibrio japonicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Jahn, M. / Stoll, D. / Warren, R.A.J. / Szabo, L. / Singh, P. / Gilbert, H.J. / Ducros, V.M.A. / Davies, G.J. / Withers, S.G. | |||||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2003 Title: Expansion of the Glycosynthase Repertoire to Produce Defined Manno-Oligosaccharides Authors: Jahn, M. / Stoll, D. / Warren, R.A.J. / Szabo, L. / Singh, P. / Gilbert, H.J. / Ducros, V.M.A. / Davies, G.J. / Withers, S.G. | |||||||||
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 | 1odz.cif.gz | 345.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1odz.ent.gz | 279.9 KB | Display | PDB format |
PDBx/mmJSON format | 1odz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/1odz ftp://data.pdbj.org/pub/pdb/validation_reports/od/1odz | HTTPS FTP |
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-Related structure data
Related structure data | 1j9yS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
NCS oper: (Code: given Matrix: (-0.99926, 0.03833, -0.00157), Vector: |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 43675.582 Da / Num. of mol.: 2 / Fragment: RESIDUES 39-423 / Mutation: E320G Source method: isolated from a genetically manipulated source Details: COMPLEX WITH MANNOBIOSE / Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Gene: manA, man26A, CJA_2770 / Plasmid: PET21A / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P49424, mannan endo-1,4-beta-mannosidase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 1039 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | RESIDUES 1-28 COMPRISE THE SIGNAL PEPTIDE. MATURE CRYSTALLISED FORM OF MAN26A E320G MUTANT CONSISTS ...RESIDUES 1-28 COMPRISE THE SIGNAL PEPTIDE. MATURE CRYSTALLIS | |
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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: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 7.5 Details: 100MM TRIS 7.5, 26% PEG550, 9MM ZNSO4, 10MM MANNOTETRAOSE, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→15 Å / Num. obs: 171242 / % possible obs: 93.7 % / Redundancy: 4.01 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.21 / % possible all: 64.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J9Y Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.961 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / 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: 13.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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