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Yorodumi- PDB-6jvv: Crystal structure of maleylpyruvate hydrolase from Sphingobium.sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jvv | ||||||
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Title | Crystal structure of maleylpyruvate hydrolase from Sphingobium.sp SYK-6 | ||||||
Components | maleylpyruvate hydrolase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingobium sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Hong, H. / Kim, K.-J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural insights into a maleylpyruvate hydrolase from sphingobium sp. SYK-6, a bacterium degrading lignin-derived aryls. Authors: Hong, H. / Seo, H. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jvv.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jvv.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jvv_validation.pdf.gz | 486.1 KB | Display | wwPDB validaton report |
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Full document | 6jvv_full_validation.pdf.gz | 493.1 KB | Display | |
Data in XML | 6jvv_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 6jvv_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/6jvv ftp://data.pdbj.org/pub/pdb/validation_reports/jv/6jvv | HTTPS FTP |
-Related structure data
Related structure data | 6jvwC 4pfzS 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: 33277.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. (strain NBRC 103272 / SYK-6) (bacteria) Strain: NBRC 103272 / SYK-6 / Gene: SLG_11280 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2IPX5 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.24 Å3/Da / Density % sol: 45.14 % / Mosaicity: 0.473 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 91240 / % possible obs: 97.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Χ2: 1.62 / Net I/σ(I): 13 / Num. measured all: 562926 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PFZ Resolution: 1.51→31.63 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.136 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 104.13 Å2 / Biso mean: 19.236 Å2 / Biso min: 9.72 Å2
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Refinement step | Cycle: final / Resolution: 1.51→31.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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