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Yorodumi- PDB-3kh8: Crystal structure of MaoC-like dehydratase from Phytophthora Capsici -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kh8 | ||||||
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Title | Crystal structure of MaoC-like dehydratase from Phytophthora Capsici | ||||||
Components | MaoC-like dehydratase | ||||||
Keywords | LYASE / Hot dog domain | ||||||
Function / homology | MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / MaoC-like dehydratase Function and homology information | ||||||
Biological species | Phytophthora Capsici (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, H. / Zhang, K. / Guo, J. / Zhou, Q. / Zheng, X. / Sun, F. / Pang, H. / Zhang, X. | ||||||
Citation | Journal: To be Published Title: Crystal structure of MaoC-like dehydratase from Phytophthora Capsici Authors: Wang, H. / Zhang, K. / Guo, J. / Zhou, Q. / Zheng, X. / Sun, F. / Pang, H. / Zhang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kh8.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kh8.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 3kh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/3kh8 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/3kh8 | HTTPS FTP |
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-Related structure data
Related structure data | 1s9cS 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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Unit cell |
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-Components
#1: Protein | Mass: 36375.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora Capsici (eukaryote) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: E3T2G3*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Water | ChemComp-HOH / | Sequence details | THE AUTHOR HAS ALREADY SUBMITTED THE SEQUENCE TO GENBANK, AND THE ID IS GU190361. IT WILL BE ...THE AUTHOR HAS ALREADY SUBMITTED THE SEQUENCE TO GENBANK, AND THE ID IS GU190361. IT WILL BE APPEARED IN UNP DATABASE SOON. | |
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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: 2.87 Å3/Da / Density % sol: 57.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes, 6% PEG6000, 5% (+/-)-2-methy-2,4-pentanediol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2009 |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→31.49 Å / Num. all: 63785 / Num. obs: 62446 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.56 / Num. unique all: 3007 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S9C Resolution: 2→31.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.206 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.668 Å2
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Refinement step | Cycle: LAST / Resolution: 2→31.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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