+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+57 | ||||||
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Title | Crystal structure of Mycobacterium smegmatis AmtR | ||||||
Components | Transcription regulator AmtR | ||||||
Keywords | TRANSLATION / HTH DNA binding motif / ligand binding domain / TetR / nitrogen regulation | ||||||
Function / homology | Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / ACETATE ION / Transcription regulator AmtR Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å | ||||||
Authors | Vickers, C.J. / McKenzie, J.L. / Arcus, V.L. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Structure and Function of AmtR in Mycobacterium smegmatis: Implications for Post-Transcriptional Regulation of Urea Metabolism through a Small Antisense RNA. Authors: Petridis, M. / Vickers, C. / Robson, J. / McKenzie, J.L. / Bereza, M. / Sharrock, A. / Aung, H.L. / Arcus, V.L. / Cook, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e57.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e57.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 5e57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e57_validation.pdf.gz | 461.9 KB | Display | wwPDB validaton report |
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Full document | 5e57_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 5e57_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 5e57_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e57 ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e57 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23606.516 Da / Num. of mol.: 3 / Fragment: UNP residues 14-225 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_4300, MSMEI_4199 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: A0R089 #2: Chemical | #3: 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: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Na acetate, Na formate, / PH range: 5.0-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 14, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.98→37.25 Å / Num. obs: 50329 / % possible obs: 97.1 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.043 / Net I/σ(I): 9.6 / Num. measured all: 336413 / Scaling rejects: 456 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→37.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2413 / WRfactor Rwork: 0.1977 / FOM work R set: 0.7973 / SU B: 4.715 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1684 / SU Rfree: 0.1579 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.158 / 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: 85.83 Å2 / Biso mean: 29.119 Å2 / Biso min: 14.94 Å2
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Refinement step | Cycle: final / Resolution: 1.98→37.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.981→2.032 Å / Total num. of bins used: 20
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