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Yorodumi- PDB-4ybn: Structure of the FAD and Heme binding protein msmeg_4975 from Myc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ybn | ||||||
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Title | Structure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis | ||||||
Components | Flavin-nucleotide-binding protein | ||||||
Keywords | OXIDOREDUCTASE / FAD / Heme / split beta-barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ahmed, F.H. / Carr, P.D. / Jackson, C.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. Authors: Ahmed, F.H. / Carr, P.D. / Lee, B.M. / Afriat-Jurnou, L. / Mohamed, A.E. / Hong, N.S. / Flanagan, J. / Taylor, M.C. / Greening, C. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ybn.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ybn.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ybn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ybn_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4ybn_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4ybn_validation.xml.gz | 25 KB | Display | |
Data in CIF | 4ybn_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4ybn ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4ybn | HTTPS FTP |
-Related structure data
Related structure data | 4y9iC 4zkyC 5bncC 2furS 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, 2 molecules AB
#1: Protein | Mass: 23786.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_4975, MSMEI_4848, LJ00_24605 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R238 |
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-Non-polymers , 6 types, 333 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Chemical | #7: 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: 2.48 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 20% PEG1500, 4% MPD, 0.1 M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9655 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9655 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→44.73 Å / Num. obs: 35306 / % possible obs: 99.6 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13 / Num. measured all: 264436 / Scaling rejects: 2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 2FUR Resolution: 1.9→44.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.124 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.145 / 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: 96.73 Å2 / Biso mean: 33.33 Å2 / Biso min: 15.37 Å2
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Refinement step | Cycle: final / Resolution: 1.9→44.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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