+Open data
-Basic information
Entry | Database: PDB / ID: 6jrd | ||||||
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Title | ZHD complex with hydrolyzed beta-ZOL | ||||||
Components | Zearalenone hydrolase | ||||||
Keywords | HYDROLASE / LACTONASE / ALPHA-BETA FOLD / ZEARALENONE DEGRADE | ||||||
Function / homology | alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Chem-C1U / : / Zearalenone hydrolase Function and homology information | ||||||
Biological species | Clonostachys rosea (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Hu, X.J. | ||||||
Citation | Journal: To Be Published Title: Structure of ZHD complex Authors: Hu, X.J. / Zhou, H.J. / Li, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jrd.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jrd.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/6jrd ftp://data.pdbj.org/pub/pdb/validation_reports/jr/6jrd | HTTPS FTP |
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-Related structure data
Related structure data | 6jqzC 6jr2C 6jr5C 6jr9C 6jraC 6jrbC 6jrcC 5c8zS 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
#1: Protein | Mass: 31018.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clonostachys rosea (fungus) / Gene: zhd101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NKB0 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE STRAIN OF CLONOSTACH | |
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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: 3.05 Å3/Da / Density % sol: 59.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium phosphate, imidazole, potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. obs: 91529 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.65→1.68 Å / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.54 / Num. unique obs: 4495 / CC1/2: 0.953 / Rpim(I) all: 0.14 / Rrim(I) all: 0.523 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C8Z Resolution: 1.65→35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.105 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→35 Å
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Refine LS restraints |
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