+Open data
-Basic information
Entry | Database: PDB / ID: 2vyx | ||||||
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Title | Crystal structure of the T. thermophilus dodecin W38F mutant | ||||||
Components | TTHA1431 | ||||||
Keywords | FLAVOPROTEIN / DODECINS / COENZYME A / FLAVIN DIMER / HYPOTHETICAL PROTEIN / FLAVIN BINDING PROTEIN / PROTEIN BINDING PUTATIVE STORAGE PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Essen, L.-O. / Meissner, B. | ||||||
Citation | Journal: To be Published Title: Ultrafast Charge Transfer Dynamics in Flavoprotein Dodecin Authors: Gurzadyan, G.G. / Meissner, B. / Sander, B. / Essen, L.-O. / Michel-Beyerle, M.E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 35-STRANDED BARREL THIS IS REPRESENTED BY A 36-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 | 2vyx.cif.gz | 203.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vyx.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vyx ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vyx | HTTPS FTP |
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-Related structure data
Related structure data | 2v18S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 7720.895 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q5SIE3 |
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-Non-polymers , 5 types, 561 molecules
#2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-COA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, TRP 38 TO PHE ENGINEERED RESIDUE IN CHAIN B, TRP 38 TO PHE ...ENGINEERED |
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Nonpolymer details | COENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEOTIDE ...COENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.2, 22.5 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 16, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→9.99 Å / Num. obs: 178447 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V18 Resolution: 1.5→9.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.376 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.092 / 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: 18.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→9.99 Å
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Refine LS restraints |
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