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- PDB-3op6: Crystal structure of an oligo-nucleotide binding protein (lpg1207... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3op6 | ||||||
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Title | Crystal structure of an oligo-nucleotide binding protein (lpg1207) from Legionella pneumophila subsp. pneumophila str. philadelphia 1 at 2.00 A resolution | ||||||
![]() | Uncharacterized protein | ||||||
![]() | UNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / OLIGO-NUCLEOTIDE BINDING PROTEIN | ||||||
Function / homology | YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / aminoacyl-tRNA editing activity / Alpha-Beta Complex / Alpha Beta / tRNA_edit domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of an oligo-nucleotide binding protein (lpg1207) from Legionella pneumophila subsp. pneumophila str. philadelphia 1 at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125 KB | Display | ![]() |
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PDB format | ![]() | 101.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.7 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION. |
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Components
#1: Protein | Mass: 16767.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1207 / Plasmid: SpeedET / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.4000M Na3Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 23, 2010 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→29.877 Å / Num. all: 20475 / Num. obs: 20475 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.097 Å2 / Rsym value: 0.114 / Net I/σ(I): 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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. 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT CONDITION IS MODELED INTO THE STRUCTURE. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4, NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
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Displacement parameters | Biso max: 111.25 Å2 / Biso mean: 40.8756 Å2 / Biso min: 8.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.877 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.11 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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