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- PDB-2bm4: The Structure of MfpA (Rv3361c, C2 Crystal form). The Pentapeptid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bm4 | ||||||
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Title | The Structure of MfpA (Rv3361c, C2 Crystal form). The Pentapeptide Repeat Protein from Mycobacterium tuberculosis Folds as A Right- handed Quadrilateral Beta-helix. | ||||||
![]() | PENTAPEPTIDE REPEAT FAMILY PROTEIN | ||||||
![]() | PENTAPEPTIDE REPEAT PROTEIN / PENTAPEPTIDE REPEAT PROTEINS / FLUROQUINOLONE RESISTANCE / DNA GYRASE / DNA MIMICRY / RIGHT-HANDED QUADRILATERAL BETA-HELIX | ||||||
Function / homology | ![]() DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / response to antibiotic / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hegde, S.S. / Vetting, M.W. / Roderick, S.L. / Mitchenall, L.A. / Maxwell, A. / Takiff, H.E. / Blanchard, J.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
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PDB format | ![]() | 61 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #2: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.43 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 400, 100 MM AMMONIUM CITRATE PH 5.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
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: 2.2→30 Å / Num. obs: 17270 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.8 / % possible all: 85.5 |
Reflection | *PLUS Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 85.5 % / Rmerge(I) obs: 0.13 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PREVIOUS STRUCTURE DETERMINED BY SE-MET MAD Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 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 THEREFORE WERE NOT MODELED.
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Solvent computation | Solvent model: BULK SOLVENT / Bsol: 54.7426 Å2 / ksol: 0.362602 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.203 / Total num. of bins used: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |