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- PDB-6aca: Crystal structure of Mycobacterium tuberculosis Mfd at 3.6 A reso... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aca | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis Mfd at 3.6 A resolution | ||||||
![]() | Mycobacterium tuberculosis Mfd | ||||||
![]() | HYDROLASE / Transcription repair coupling factor / Mfd / Transcription regulation / Transcription Coupled Nucleotide Excision Repair. | ||||||
Function / homology | ![]() transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / DNA translocase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / regulation of DNA-templated transcription / DNA binding / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Putta, S. / Fox, G.C. / Walsh, M.A. / Rao, D.N. / Nagaraja, V. / Natesh, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for nucleotide-mediated remodelling mechanism of Mycobacterium Mfd Authors: Putta, S. / Prabha, S. / Bhat, V. / Fox, G.C. / Walsh, M.A. / Rao, D.N. / Nagaraja, V. / Natesh, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.8 KB | Display | ![]() |
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PDB format | ![]() | 172.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 54.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9614C ![]() 6ac6C ![]() 6ac8SC ![]() 6acxC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 135239.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H37Rv / Gene: mfd / Plasmid: pETMtbMfd / Details (production host): MtbMfd gene cloned into pET28a / Production host: ![]() ![]() References: UniProt: P9WMQ5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.6 % / Description: Cubic |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM HEPES Sodium pH 7.0, 800mM Ammonium Formate, 20% PEG3350, 7.5mM MgCl2.6H2O PH range: 7.0-7.5 / Temp details: Rubarth Incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryo Stream |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2015 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→39.64 Å / Num. obs: 22846 / % possible obs: 99.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 110.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.052 / Rrim(I) all: 0.159 / Rsym value: 0.149 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.6→3.89 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.006 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4588 / CC1/2: 0.381 / Rpim(I) all: 0.382 / Rrim(I) all: 1.141 / Rsym value: 1.069 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6AC8 Resolution: 3.6→39.64 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Details: Phenix refinement
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Displacement parameters | Biso mean: 114.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→39.64 Å
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Refine LS restraints |
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LS refinement shell |
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