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Yorodumi- PDB-4qoa: Crystal structure of a putative periplasmic protein (BACUNI_04550... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qoa | ||||||
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Title | Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution | ||||||
Components | Putative periplasmic proteinPeriplasm | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two copies of DUF2874 domain (PF11396) / BLIP-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Inhibitor of vertebrate lysozyme, Ivy - #30 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / Alpha Beta / PepSY_like domain-containing protein Function and homology information | ||||||
Biological species | Bacteroides uniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 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 | 4qoa.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qoa.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/4qoa ftp://data.pdbj.org/pub/pdb/validation_reports/qo/4qoa | HTTPS FTP |
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-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: 14669.667 Da / Num. of mol.: 1 / Fragment: UNP residues 21-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: BACUNI_04550 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7VAB9 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.77 Å3/Da / Density % sol: 74.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 24.00% polyethylene glycol 3350, 0.16M tri-ammonium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9116,0.9794,0.9793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2014 Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.75→29.823 Å / Num. all: 7860 / Num. obs: 7860 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rsym value: 0.084 / Net I/σ(I): 15.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.012 / 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: 2.75→29.823 Å / Cor.coef. Fo:Fc: 0.9249 / Cor.coef. Fo:Fc free: 0.9142 / Occupancy max: 1 / Occupancy min: 0.75 / 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 THE REFINEMENT. 4. 1,2-ETHANEDIOL USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE.
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Displacement parameters | Biso max: 158.89 Å2 / Biso mean: 87.8228 Å2 / Biso min: 50.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.535 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→29.823 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→3.07 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 28.7089 Å / Origin y: 24.7284 Å / Origin z: 28.5723 Å
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