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Yorodumi- PDB-4awu: Crystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4awu | ||||||
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Title | Crystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE1) M25L mutant in complex with para-chlorophenol | ||||||
Components | OXIDOREDUCTASE, FMN-BINDING | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SHEWANELLA ONEIDENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Elegheert, J. / Brige, A. / Savvides, S.N. | ||||||
Citation | Journal: To be Published Title: Modulation of Isoalloxazine Ring Planarity Influences Fmn Electronic Properties in Old Yellow Enzymes Authors: Elegheert, J. / Pauwels, E. / Wille, G. / Brige, A. / Savvides, S.N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4awu.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4awu.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 4awu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4awu_validation.pdf.gz | 984.4 KB | Display | wwPDB validaton report |
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Full document | 4awu_full_validation.pdf.gz | 985.8 KB | Display | |
Data in XML | 4awu_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4awu_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/4awu ftp://data.pdbj.org/pub/pdb/validation_reports/aw/4awu | HTTPS FTP |
-Related structure data
Related structure data | 4awsSC 4awtC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39613.543 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Strain: MR-1 / Plasmid: PACYC-DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EEC8, NADPH dehydrogenase |
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-Non-polymers , 5 types, 411 molecules
#2: Chemical | ChemComp-FMN / | ||||
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#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-PE4 / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED |
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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: 2.22 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 100 MM TRIS PH 8.2, 1.65 M (NH4)2SO4, 2 % PEG400 AND 0.25 % (W/V) BETA-OCTYL GLUCOSIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8015 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8015 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→42 Å / Num. obs: 40083 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 16.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AWS Resolution: 1.69→41.997 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10 Å2 / ksol: 0.5 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→41.997 Å
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Refine LS restraints |
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LS refinement shell |
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