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Yorodumi- PDB-6j4d: Crystal structure of MarH, an epimerase for biosynthesis of Marem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j4d | ||||||||||||
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Title | Crystal structure of MarH, an epimerase for biosynthesis of Maremycins in Streptomyces, under pH 4.7, without Zn | ||||||||||||
Components | Cupin superfamily protein | ||||||||||||
Keywords | ISOMERASE / epimerase / Maremycins / biosynthesis | ||||||||||||
Function / homology | RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / CITRATE ANION / Cupin superfamily protein Function and homology information | ||||||||||||
Biological species | Streptomyces sp. B9173 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Hou, Y. / Liu, B. / Hu, K. / Zhang, R. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Structural Basis for the Isomerization Mechanism of MarH Authors: Liu, B. / Hou, Y. / Zhang, R. / Hu, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j4d.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j4d.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 6j4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j4d_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 6j4d_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 6j4d_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 6j4d_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/6j4d ftp://data.pdbj.org/pub/pdb/validation_reports/j4/6j4d | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 13323.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. B9173 (bacteria) / Gene: marH / Production host: Escherichia coli (E. coli) / References: UniProt: X2D812 |
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#2: Chemical | ChemComp-FLC / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 100mM sodium citrate, pH4.7, 20% PEG3350, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97891 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 18801 / % possible obs: 98.5 % / Redundancy: 14 % / Net I/σ(I): 54.3 |
Reflection shell | Resolution: 1.4→1.42 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→37.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.757 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / 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: 85.6 Å2 / Biso mean: 10.862 Å2 / Biso min: 4.71 Å2
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Refinement step | Cycle: final / Resolution: 1.4→37.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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