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Yorodumi- PDB-3ot2: Crystal structure of a putative nuclease belonging to DUF820 (Ava... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ot2 | ||||||
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Title | Crystal structure of a putative nuclease belonging to DUF820 (Ava_3926) from Anabaena variabilis ATCC 29413 at 1.96 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural Genomics / UNKNOWN FUNCTION / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information tt1808, chain A / Putative restriction endonuclease / Putative restriction endonuclease / tt1808, chain A / Restriction endonuclease type II-like / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Anabaena variabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative nuclease belonging to DUF820 (Ava_3926) from Anabaena variabilis ATCC 29413 at 1.96 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 | 3ot2.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ot2.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ot2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/3ot2 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/3ot2 | 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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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21341.908 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / PCC 7937 / Gene: Ava_3926 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M655 |
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-Non-polymers , 5 types, 294 molecules
#2: Chemical | #3: Chemical | ChemComp-BU1 / | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.17 % |
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Crystal grow | Temperature: 277 K / pH: 4.14 Details: 30.40% 1,4-butanediol, 0.1M sodium acetate pH 4.14, 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: BL9-2 / Wavelength: 0.97907 |
Detector | Type: MAR MAR325 / Detector: CCD / Date: Mar 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→48.826 Å / Num. obs: 41141 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.33 Å2 |
Reflection shell | Resolution: 1.96→2.03 Å / Rmerge(I) obs: 1.546 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.96→48.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 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. 2.1,4-BUTANEDIOL (BU1), CHLORIDE (CL), ETHYLENE GLYCOL (EDO) AND ACETATE (ACT) MODELED ARE PRESENT PROTEIN/ CRYSTALLIZATION/CRYO BUFFER. 3.RESIDUES OF 8-106 OF CHAIN B ARE NOT WELL ORDERED, THE MODEL WAS GENERATED BASED ON A CHAIN. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Displacement parameters | Biso mean: 55.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→48.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.01 Å
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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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