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Yorodumi- PDB-4qrl: Crystal structure of a lipocalin-like protein (BACUNI_01346) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qrl | ||||||
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Title | Crystal structure of a lipocalin-like protein (BACUNI_01346) from Bacteroides uniformis ATCC 8492 at 1.79 A resolution | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lipocalin-like protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Lipocalin-like domain / Lipocalin - #280 / Lipocalin-like domain / Lipocalin / Beta Barrel / Mainly Beta / Lipocalin-like domain-containing protein Function and homology information | ||||||
Biological species | Bacteroides uniformis ATCC 8492 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a hypothetical protein (BACUNI_01346) from Bacteroides uniformis ATCC 8492 at 1.79 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 | 4qrl.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qrl.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qrl_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 4qrl_full_validation.pdf.gz | 423 KB | Display | |
Data in XML | 4qrl_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 4qrl_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/4qrl ftp://data.pdbj.org/pub/pdb/validation_reports/qr/4qrl | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13112.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis ATCC 8492 (bacteria) Gene: BACUNI_01346, ZP_02069929.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V1A8 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (21-135) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (21-135) WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M calcium chloride, 20.0% 2-propanol, 10.0% 1,2-butanediol, 0.1M sodium acetate pH 4.6, 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: BL11-1 / Wavelength: 0.91837 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91837 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→39.225 Å / Num. obs: 10664 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.34 % / Biso Wilson estimate: 28.043 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→39.225 Å / Cor.coef. Fo:Fc: 0.9636 / Cor.coef. Fo:Fc free: 0.9302 / Occupancy max: 1 / Occupancy min: 0.35 / 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. EDO MODELED WAS PRESENT IN CRYO CONDITION. 4. THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT.
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Displacement parameters | Biso max: 98.29 Å2 / Biso mean: 33.9279 Å2 / Biso min: 18.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.207 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→39.225 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→2 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 9.5385 Å / Origin y: 27.6457 Å / Origin z: 12.1177 Å
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Refinement TLS group | Selection details: {A|26 - 135} |