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Yorodumi- PDB-1vlq: Crystal structure of Acetyl xylan esterase (TM0077) from Thermoto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vlq | ||||||
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Title | Crystal structure of Acetyl xylan esterase (TM0077) from Thermotoga maritima at 2.10 A resolution | ||||||
Components | acetyl xylan esterase | ||||||
Keywords | HYDROLASE / TM0077 / ACETYL XYLAN ESTERASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics | ||||||
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 / MAD / Resolution: 2.1 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 | 1vlq.cif.gz | 799.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vlq.ent.gz | 670 KB | Display | PDB format |
PDBx/mmJSON format | 1vlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/1vlq ftp://data.pdbj.org/pub/pdb/validation_reports/vl/1vlq | HTTPS FTP |
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-Related structure data
Related structure data | 3m81C 3m82C 3m83C 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 label comp-ID: PHE / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 4 - 320 / Label seq-ID: 16 - 332
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-Components
#1: Protein | Mass: 38991.184 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0077 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXT2, cephalosporin-C deacetylase #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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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: 2.93 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2 Details: 20% PEG-300, 10% glycerol, 0.1M Phosphate-citrate pH 4.2 0.2 M (NH4)2SO4 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2001 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→29.56 Å / Num. obs: 293140 / % possible obs: 93 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.49 Å2 / Rsym value: 0.09 / Net I/σ(I): 9.1 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 30908 / Rsym value: 0.433 / % possible all: 67.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→29.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.076 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.17 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE ACTIVE SITE TRIAD CONSISTS OF SER188, HIS303 AND ASP274. THE ELECTRON DENSITY SUGGESTED THERE COULD EXIST A PARTIALLY OCCUPIED ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE ACTIVE SITE TRIAD CONSISTS OF SER188, HIS303 AND ASP274. THE ELECTRON DENSITY SUGGESTED THERE COULD EXIST A PARTIALLY OCCUPIED ACYL INTERMEDIATE ON SER188. HOWEVER, IT IS NOT CONCLUSIVE. AS A RESULT, WATER MOLECULES WERE MODELLED. 3. THERE IS SOME UNEXPLAINED DENSITY NEAR N-TERMINUS 4. RESIDUES 134,135 OF CHAIN D,H,I,J,K,L HAVE POOR DENSITY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.959 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.56 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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