+Open data
-Basic information
Entry | Database: PDB / ID: 2yiz | ||||||
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Title | X-ray structure of Mycobacterium tuberculosis Dodecin | ||||||
Components | DODECIN | ||||||
Keywords | FLAVOPROTEIN / FLAVIN BINDING PROTEIN / PROTEIN-ENGINEERING / PUTATIVE STORAGE PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Vinzenz, X. / Grosse, W. / Linne, U. / Meissner, B. / Essen, L.-O. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2011 Title: Chemical Engineering of Mycobacterium Tuberculosis Dodecin Hybrids. Authors: Vinzenz, X. / Grosse, W. / Linne, U. / Meissner, B. / Essen, L.-O. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yiz.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yiz.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/2yiz ftp://data.pdbj.org/pub/pdb/validation_reports/yi/2yiz | HTTPS FTP |
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-Related structure data
Related structure data | 2yj0C 2v21S 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 7506.432 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-70 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q8VK10 |
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-Non-polymers , 6 types, 277 molecules
#2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | COENZYME A (COA): NON-COVALENTLY BOUND, NOT COMPLETELY DEFINED IN DENSITY AND THEREFORE ONLY PARTLY ...COENZYME A (COA): NON-COVALENTLY |
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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: 3.18 Å3/Da / Density % sol: 61.37 % / Description: NONE |
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Crystal grow | pH: 5 Details: 10 MM CO CL2, 100 MM NAOAC PH 5.0, 200 MM HEXANEDIOL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Feb 17, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→14.91 Å / Num. obs: 43832 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V21 Resolution: 1.7→14.91 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.046 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COA ALONG THREEFOLD AXIS WAS ONLY PARTLY DEFINED IN ELECTRON DENSITY AND THEREFORE ONLY PARTLY REFINED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→14.91 Å
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Refine LS restraints |
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