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Yorodumi- PDB-3gw2: Crystal structure of possible transcriptional regulatory protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gw2 | ||||||
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Title | Crystal structure of possible transcriptional regulatory protein (fragment 1-100) from Mycobacterium bovis. Northeast Structural Genomics Consortium Target MbR242E. | ||||||
Components | Possible transcriptional regulatory arsR-family protein | ||||||
Keywords | TRANSCRIPTION REGULATOR / Structural Genomics / PSI-2 / Protein Structure Initiative / MbR242E / Q7U294 / Northeast Structural Genomics Consortium / NESG / DNA-binding / Transcription / Transcription regulation / Transferase | ||||||
Function / homology | Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Mycobacterium bovis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Kuzin, A.P. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be published Title: Northeast Structural Genomics Consortium Target MbR242E Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gw2.cif.gz | 26.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gw2.ent.gz | 20.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gw2_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 3gw2_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 3gw2_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 3gw2_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/3gw2 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/3gw2 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11840.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium bovis (bacteria) / Strain: AF2122/97 / Gene: Mb0332 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7U294 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl pH 7.5. Reservoir solution: 22% PEG 4000, 0.1M Bis-Tris pH 7.2, 0.1M NH4H2PO4, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97900, 0.97928, 0.96785 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2009 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si(111) CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 16969 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 27.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 62.8 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 27.7 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 12.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→19.72 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.635 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.778 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 29.2267 Å / Origin y: 29.8025 Å / Origin z: 28.5716 Å
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Refinement TLS group |
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