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Yorodumi- PDB-4m0h: Crystal structure of a putative anti-sigma factor (BDI_1681) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m0h | ||||||
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Title | Crystal structure of a putative anti-sigma factor (BDI_1681) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution | ||||||
Components | Conserved hypothetical protein, putative anti-sigma factor | ||||||
Keywords | SIGNALING PROTEIN / FecR protein / PF04773 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Parabacteroides distasonis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a conserved hypothetical protein, putative anti-sigma factor (BDI_1681) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m0h.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m0h.ent.gz | 148.3 KB | Display | PDB format |
PDBx/mmJSON format | 4m0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m0h_validation.pdf.gz | 446.2 KB | Display | wwPDB validaton report |
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Full document | 4m0h_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 4m0h_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4m0h_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/4m0h ftp://data.pdbj.org/pub/pdb/validation_reports/m0/4m0h | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26760.070 Da / Num. of mol.: 2 / Fragment: UNP residues 107-337 / Mutation: T199G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_1681 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LCL9 #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 107-337) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THE CONSTRUCT (RESIDUES 107-337) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
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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: 2.64 Å3/Da / Density % sol: 53.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 4.300M sodium chloride, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97963, 0.9791 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→29.449 Å / Num. all: 20436 / Num. obs: 20436 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rsym value: 0.11 / Net I/σ(I): 11.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→29.449 Å / Cor.coef. Fo:Fc: 0.9389 / Cor.coef. Fo:Fc free: 0.9243 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.CHLORIDE IONS (CL) FROM THE CRYSTALLIZATION AND GLYCEROL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
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Displacement parameters | Biso max: 133.42 Å2 / Biso mean: 46.8176 Å2 / Biso min: 19.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.304 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.449 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.63 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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