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Yorodumi- PDB-4hbr: Crystal structure of a putative periplasmic proteins (BACEGG_0142... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hbr | ||||||
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Title | Crystal structure of a putative periplasmic proteins (BACEGG_01429) from Bacteroides eggerthii DSM 20697 at 2.40 A resolution | ||||||
Components | Putative periplasmic protein | ||||||
Keywords | Structural Genomics / Unknown Function / beta lactamase like fold / DUF2874 / PF11396 family protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Nuclear Transport Factor 2; Chain: A, - #360 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / : Function and homology information | ||||||
Biological species | Bacteroides eggerthii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative periplasmic proteins (BACEGG_01429) from Bacteroides eggerthii DSM 20697 at 2.40 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 | 4hbr.cif.gz | 241.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hbr.ent.gz | 200.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hbr_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 4hbr_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 4hbr_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4hbr_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/4hbr ftp://data.pdbj.org/pub/pdb/validation_reports/hb/4hbr | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16014.239 Da / Num. of mol.: 4 / Fragment: UNP residues 22-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_01429, ZP_03458652.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AGA3 #2: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (22-160) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-160) WAS EXPRESSED WITH A 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: 4.68 Å3/Da / Density % sol: 73.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.20M magnesium chloride, 10.00% polyethylene glycol 3000, 0.1M sodium cacodylate pH 6.5, 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: BL14-1 / Wavelength: 0.97923 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 9, 2012 Details: Vertical focusing mirror; double crystal Si(111) monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→29.41 Å / Num. all: 47503 / Num. obs: 47503 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 52.511 Å2 / Rsym value: 0.102 / Net I/σ(I): 11.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→29.41 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.9235 / 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).
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Displacement parameters | Biso max: 193.97 Å2 / Biso mean: 58.5116 Å2 / Biso min: 26.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.368 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
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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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