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Yorodumi- PDB-1up6: Structure of the 6-phospho-beta glucosidase from Thermotoga marit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1up6 | ||||||
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Title | Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate | ||||||
Components | 6-PHOSPHO-BETA-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / 6-PHOSPHO-BETA-GLUCOSIDASE / FAMILY4 HYDROLASE / NAD DEPENDENT | ||||||
Function / homology | Function and homology information 6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / : / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Varrot, A. / Yip, V.L. / Withers, S.G. / Davies, G.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2004 Title: An Unusual Mechanism of Glycoside Hydrolysis Involving Redox and Elimination Steps by a Family 4 Beta-Glycosidase from Thermotoga Maritima. Authors: Yip, V.L. / Varrot, A. / Davies, G.J. / Rajan, S.S. / Yang, X. / Thompson, J. / Anderson, W.F. / 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 | 1up6.cif.gz | 646.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1up6.ent.gz | 534.6 KB | Display | PDB format |
PDBx/mmJSON format | 1up6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1up6_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1up6_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1up6_validation.xml.gz | 65 KB | Display | |
Data in CIF | 1up6_validation.cif.gz | 102.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1up6 ftp://data.pdbj.org/pub/pdb/validation_reports/up/1up6 | HTTPS FTP |
-Related structure data
Related structure data | 1up4S 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: Component-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 2 / Auth seq-ID: 1 - 415 / Label seq-ID: 2 - 416
NCS ensembles :
NCS oper:
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-Components
-Protein / Sugars , 2 types, 10 molecules ABCDEFGH
#1: Protein | Mass: 48160.117 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: SYNTHETIC GENE / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9X108, EC: 3.2.1.6 #4: Sugar | |
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-Non-polymers , 4 types, 580 molecules
#2: Chemical | #3: Chemical | ChemComp-MN / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | HIS 0, PART OF THE INSERTED N-TERMINAL HIS 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: 2.8 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | pH: 4.6 Details: 200 MM SODIUM FORMATE, 100MM SODIUM ACETATE PH 4.6, 5% PEG 4000. PROTEIN AT 5 MG/ML |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Date: Dec 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. obs: 149303 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UP4 Resolution: 2.55→19.96 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.719 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY AND ATOM HAVE BEEN GIBEN AN OCCUPANCY OF 0.0
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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: 20.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→19.96 Å
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Refine LS restraints |
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