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Yorodumi- PDB-3m82: Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m82 | ||||||
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Title | Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.40 A resolution (PMSF inhibitor complex structure) | ||||||
Components | Acetyl xylan esterase | ||||||
Keywords | HYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / AXE1 | ||||||
Function / homology | Function and homology information xylan metabolic process / cephalosporin C metabolic process / cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / polysaccharide metabolic process / acetylxylan esterase / acetylxylan esterase activity / carboxylic ester hydrolase activity / cellulose catabolic process / calcium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Proteins / Year: 2012 Title: Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima. Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / ...Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / Deacon, A.M. / van der Oost, J. / Lesley, S.A. / Elsliger, M.A. / Kengen, S.W. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m82.cif.gz | 413.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m82.ent.gz | 336.5 KB | Display | PDB format |
PDBx/mmJSON format | 3m82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/3m82 ftp://data.pdbj.org/pub/pdb/validation_reports/m8/3m82 | HTTPS FTP |
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-Related structure data
Related structure data | 1vlqSC 3m81C 3m83C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 3 - 323 / Label seq-ID: 15 - 335
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Details | AUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION FOR THE UNCOMPLEXED PROTEIN. |
-Components
#1: Protein | Mass: 38817.105 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0077, TM_0077 / Plasmid: MH1 / Production host: Escherichia Coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9WXT2 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, Additive: 0.004 M phenylmethylsulfonyl fluoride (PMSF), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→48.97 Å / Num. obs: 94681 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.88 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 1vlq Resolution: 2.4→48.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.401 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE DIETHYL PHOSPHONATE (DEP) IS COVALENTALY BOUND TO THE SER 188 IN THE ACTIVE SITE OF A, B, C, D, E AND F CHAINS. 3. CALCIUM (CA) ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE DIETHYL PHOSPHONATE (DEP) IS COVALENTALY BOUND TO THE SER 188 IN THE ACTIVE SITE OF A, B, C, D, E AND F CHAINS. 3. CALCIUM (CA) AND ACETATE (ACT) IONS FROM CRYSTALLIZATION CONDITIONS, AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO CONDITION ARE MODELLED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.53 Å2 / Biso mean: 23.244 Å2 / Biso min: 2.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→48.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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