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Yorodumi- PDB-1up7: Structure of the 6-phospho-beta glucosidase from Thermotoga marit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1up7 | ||||||
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Title | Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.4 Angstrom resolution in the tetragonal form with 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 / methyl beta-D-glucoside 6-phosphate glucohydrolase 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: 2.4 Å | ||||||
Authors | Varrot, A. / Yip, V.L. / Withers, S.G. / Davies, G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Nad+ and Metal-Ion Dependent Hydrolysis by Family 4 Glycosidases: Structural Insight Into Specificity for Phospho-Beta-D-Glucosides Authors: Varrot, A. / Yip, V.L. / Li, Y. / Rajan, S.S. / Yang, X. / Anderson, W.F. / Thompson, J. / Withers, S.G. / 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 | 1up7.cif.gz | 652.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1up7.ent.gz | 550.9 KB | Display | PDB format |
PDBx/mmJSON format | 1up7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1up7 ftp://data.pdbj.org/pub/pdb/validation_reports/up/1up7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 47989.051 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 #2: Chemical | ChemComp-NAD / #3: Sugar | ChemComp-G6P / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | HIS 0, PART OF THE INSERTED N TERMINAL HIS TAG ARG -1, 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 % Description: THE STARTING MODEL USED WAS THE SELENOMET STRUCTURE SOLVED IN THE SAME SPACE GROUP |
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Crystal grow | pH: 4.6 Details: 200 MM CALCIUM ACETATE, 100MM SODIUM ACETATE PH 4.6, 25% PEG500DME, 0.2MM NAD+, 1MM PNP-BETA-D-GLUCOSE-6-PHOSPHATE, 2MM MNS04. PROTEIN AT 5 MG/ML WITH THE COFACTORS IN THE SAME CONCENTRATION AS ABOVE. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 170857 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.5 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SE-MET STRUCTURE Resolution: 2.4→19.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.116 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY AND ATOM HAVE BEEN GIVEN 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: 21.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.96 Å
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Refine LS restraints |
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