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Yorodumi- PDB-1qoz: Catalytic core domain of acetyl xylan esterase from Trichoderma reesei -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qoz | |||||||||
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Title | Catalytic core domain of acetyl xylan esterase from Trichoderma reesei | |||||||||
Components | ACETYL XYLAN ESTERASE | |||||||||
Keywords | HYDROLASE / ESTERASE / XYLAN DEGRADATION | |||||||||
Function / homology | Function and homology information acetylxylan esterase / acetylxylan esterase activity / cellulose binding / xylan catabolic process / cellulose catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | TRICHODERMA REESEI (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Hakulinen, N. / Rouvinen, J. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2000 Title: Three-Dimensional Structure of the Catalytic Core of Acetylxylan Esterase from Trichoderma Reesei: Insights Into the Deacetylation Mechanism Authors: Hakulinen, N. / Tenkanen, M. / Rouvinen, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Catalytic Core of Acetylxylan Esterase from Trichoderma Reesei Authors: Hakulinen, N. / Tenkanen, M. / Rouvinen, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qoz.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qoz.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qoz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qoz ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qoz | HTTPS FTP |
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-Related structure data
Related structure data | 1bs9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6846, 0.2911, -0.6682), Vector: |
-Components
#1: Protein | Mass: 21009.152 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-238 / Source method: isolated from a natural source / Source: (natural) TRICHODERMA REESEI (fungus) / Strain: RUTC-30 / References: UniProt: Q99034, acetylxylan esterase #2: Sugar | #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: 2.23 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.2 Details: 1.1 M POTASSIUM/SODIUM TARTRATE, 0.1 M TES, 9 MM TRITON-X, PH 8.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 8.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 15, 1998 |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→99 Å / Num. obs: 27058 / % possible obs: 87 % / Redundancy: 2.07 % / Biso Wilson estimate: 18.76 Å2 / Rsym value: 0.057 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.38 / Rsym value: 0.247 / % possible all: 46.5 |
Reflection | *PLUS % possible obs: 87 % / Num. measured all: 55958 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 47 % / Rmerge(I) obs: 0.247 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BS9 Resolution: 1.9→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 15.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 |