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Yorodumi- PDB-3zwq: HYPERTHERMOPHILIC ESTERASE FROM THE ARCHEON PYROBACULUM CALIDIFONTIS -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zwq | |||||||||
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Title | HYPERTHERMOPHILIC ESTERASE FROM THE ARCHEON PYROBACULUM CALIDIFONTIS | |||||||||
Components | ALPHA/BETA HYDROLASE FOLD-3 DOMAIN PROTEIN | |||||||||
Keywords | HYDROLASE / HYPERTHERMOPHILIC ENZYME / ESTERASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | PYROBACULUM CALIDIFONTIS (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Palm, G.J. / Bogdanovic, X. / Hinrichs, W. | |||||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2011 Title: The Crystal Structure of an Esterase from the Hyperthermophilic Microorganism Pyrobaculum Calidifontis Va1 Supports Explanation of its Enantioselectivity. Authors: Palm, G.J. / Fernandez-Alvaro, E. / Bogdanovic, X. / Bartsch, S. / Sczodrok, J. / Singh, R.K. / Boettcher, D. / Atomi, H. / Bornscheuer, U.T. / Hinrichs, W. #1: Journal: Appl.Environ.Microbiol. / Year: 2002 Title: Extremely Stable and Versatile Carboxylesterase from a Hyperthermophilic Archaeon. Authors: Hotta, Y. / Ezaki, S. / Atomi, H. / Imanaka, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zwq.cif.gz | 260.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zwq.ent.gz | 213.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/3zwq ftp://data.pdbj.org/pub/pdb/validation_reports/zw/3zwq | HTTPS FTP |
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-Related structure data
Related structure data | 2yh2C 2c7bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.95, -0.311, -0.015), Vector: |
-Components
#1: Protein | Mass: 34396.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROBACULUM CALIDIFONTIS (archaea) / Strain: VA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: A3MVR4, carboxylesterase #2: 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: 2.69 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 2 UL PROTEIN (IN 20 MM TRIS PH 8.0) PLUS 2 UL RESERVOIR (30% MPD, 10% PEG 6000, 0.1 M NAOAC). |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Sep 9, 2008 / Details: OSMIC MULTILAYER |
Radiation | Monochromator: OSMIC MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→44 Å / Num. obs: 46646 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C7B Resolution: 2→127 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.594 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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 mean: 38.399 Å2
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Refinement step | Cycle: LAST / Resolution: 2→127 Å
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Refine LS restraints |
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