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Yorodumi- PDB-2bm5: The Structure of MfpA (Rv3361c, P21 Crystal form). The Pentapepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bm5 | ||||||
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Title | The Structure of MfpA (Rv3361c, P21 Crystal form). The Pentapeptide Repeat Protein from Mycobacterium tuberculosis Folds as A Right- handed Quadrilateral Beta-helix. | ||||||
Components | PENTAPEPTIDE REPEAT FAMILY PROTEIN | ||||||
Keywords | PENTAPEPTIDE REPEAT PROTEIN / FLUROQUINOLONE RESISTANCE / DNA GYRASE / DNA MIMICRY / RIGHT-HANDED QUADRILATERAL BETA-HELIX | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / response to antibiotic / protein homodimerization activity Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hegde, S.S. / Vetting, M.W. / Roderick, S.L. / Mitchenall, L.A. / Maxwell, A. / Takiff, H.E. / Blanchard, J.S. | ||||||
Citation | Journal: Science / Year: 2005 Title: A Fluroquinolone Resistance Protein from Mycobacterium Tuberculosis that Mimics DNA Authors: Hegde, S.S. / Vetting, M.W. / Roderick, S.L. / Mitchenall, L.A. / Maxwell, A. / Takiff, H.E. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bm5.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bm5.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 2bm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bm5_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
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Full document | 2bm5_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 2bm5_validation.xml.gz | 17 KB | Display | |
Data in CIF | 2bm5_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/2bm5 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/2bm5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20325.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O50390 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Sequence details | THREE RESIDUES FROM N-TERMINAL HIS-TAG REMAIN AFTER THROMBIN CLEAVAGE OF THE TAG. | |
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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: 1.92 Å3/Da / Density % sol: 35.52 % |
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Crystal grow | pH: 5.5 Details: PROTEIN (10 MG/ML, 30 MM BETA-MERCAPTOETHANOL, 10 MM AMMONIUM CITRATE) CRYSTALLIZED IN 30% ETHYLENE GLYCOL, 100 MM CITRATE PHOSPHATE PH5.5, 200 MM AMMONIUM SULFATE., pH 5.50 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MSC RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 21905 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.4 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUS STRUCTURE DETERMINED BY SE-MET MAD Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: MISSING RESIDUES FROM MISSING RESIDUES FROM THE N AND C-TERMINI OF THE SUBMITTED COORDINATES AS COMPARED TO THE SUBMITTED SEQUENCE ARE REGIONS WHICH EXHIBITED NO ELECTRON DENSITY AND THEREFORE WERE NOT MODELED.
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Solvent computation | Solvent model: SHELL MODEL / Bsol: 41.9197 Å2 / ksol: 0.3162 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 10 /
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