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Yorodumi- PDB-6b8w: 1.9 Angstrom Resolution Crystal Structure of Cupin_2 Domain (pfam... -
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-Basic information
Entry | Database: PDB / ID: 6b8w | ||||||
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Title | 1.9 Angstrom Resolution Crystal Structure of Cupin_2 Domain (pfam 07883) of XRE Family Transcriptional Regulator from Enterobacter cloacae. | ||||||
Components | XRE family transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / XRE Family Transcriptional Regulator. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter cloacae subsp. cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Skarina, T. / McChesney, C. / Grimshaw, S. / Sandoval, J. / Satchell, K.J.F. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.9 Angstrom Resolution Crystal Structure of Cupin_2 Domain (pfam 07883) of XRE Family Transcriptional Regulator from Enterobacter cloacae. Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / McChesney, C. / Grimshaw, S. / Sandoval, J. / Satchell, K.J.F. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b8w.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b8w.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 6b8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b8w_validation.pdf.gz | 428.4 KB | Display | wwPDB validaton report |
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Full document | 6b8w_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 6b8w_validation.xml.gz | 13 KB | Display | |
Data in CIF | 6b8w_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/6b8w ftp://data.pdbj.org/pub/pdb/validation_reports/b8/6b8w | HTTPS FTP |
-Related structure data
Related structure data | 1y9qS S: Starting model for refinement |
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Similar structure data | |
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: 10807.256 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria) Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_02024 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A0H3CJW2 #2: Chemical | ChemComp-SCN / | #3: Chemical | ChemComp-MN / | #4: Water | ChemComp-HOH / | Sequence details | Authors state that the full length protein used in study was hydrolyzed during crystallization ...Authors state that the full length protein used in study was hydrolyzed during crystallization experiments, the model starts at 81th residue GLN of UniProt reference, but it is not known exactly where the protein was hydrolyzed. | |
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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: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein: 12.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.2M Sodium thiocyan, 20% (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 21115 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Rsym value: 0.074 / Χ2: 1.028 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1019 / CC1/2: 0.678 / Rpim(I) all: 0.381 / Rrim(I) all: 0.87 / Rsym value: 0.779 / Χ2: 1.029 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y9Q Resolution: 1.9→29.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.538 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.6 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.197 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→29.87 Å
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