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Yorodumi- PDB-3zho: X-ray structure of E.coli Wrba in complex with FMN at 1.2 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zho | ||||||
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Title | X-ray structure of E.coli Wrba in complex with FMN at 1.2 A resolution | ||||||
Components | FLAVOPROTEIN WRBA | ||||||
Keywords | OXIDOREDUCTASE / TRP REPRESSOR / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to oxidative stress / protein-containing complex ...NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to oxidative stress / protein-containing complex / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Kishko, I. / Lapkouski, M. / Brynda, J. / Kuty, M. / Carey, J. / Smatanova, I.K. / Ettrich, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: 1.2 A Resolution Crystal Structure of Escherichia Coli Wrba Holoprotein Authors: Kishko, I. / Carey, J. / Reha, D. / Brynda, J. / Winkler, R. / Harish, B. / Guerra, R. / Ettrichova, O. / Kukacka, Z. / Sheryemyetyeva, O. / Novak, P. / Kuty, M. / Kuta Smatanova, I. / ...Authors: Kishko, I. / Carey, J. / Reha, D. / Brynda, J. / Winkler, R. / Harish, B. / Guerra, R. / Ettrichova, O. / Kukacka, Z. / Sheryemyetyeva, O. / Novak, P. / Kuty, M. / Kuta Smatanova, I. / Ettrich, R. / Lapkouski, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zho.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zho.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 3zho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zho ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zho | HTTPS FTP |
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-Related structure data
Related structure data | 2r97S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.3612, -0.6307, -0.6868), Vector: |
-Components
#1: Protein | Mass: 20747.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A8G6, NAD(P)H dehydrogenase (quinone) #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | INITIATOR METHIONINE IS CLEAVED FROM THE MATURE WRBA PROTEIN AND RESIDUE NUMBERING IN THE STRUCTURE ...INITIATOR METHIONINE | |
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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: 1.85 Å3/Da / Density % sol: 34 % / Description: NONE |
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Crystal grow | Details: WRBA-FAD AT A CONCENTRATION OF 5 MG/ML IN 20 MM TRIS PH 6.5 CRYSTALLYZED AGAINST WELL CONTAINING 28% PEG 3350 AND 0.05 M BIS-TRIS-HCL, PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→22.7 Å / Num. obs: 97715 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R97 Resolution: 1.2→21.46 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.166 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.039 / 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: 15.468 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→21.46 Å
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