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Yorodumi- PDB-2inb: Crystal structure of an XisH family protein (ZP_00107633.1) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2inb | ||||||
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Title | Crystal structure of an XisH family protein (ZP_00107633.1) from Nostoc punctiforme PCC 73102 at 1.60 A resolution | ||||||
Components | hypothetical protein | ||||||
Keywords | Structural Genomics/Unknown function / ZP_00107633.1 / hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX | ||||||
Function / homology | Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Nostoc punctiforme (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models. Authors: Hwang, W.C. / Golden, J.W. / Pascual, J. / Xu, D. / Cheltsov, A. / Godzik, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2inb.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2inb.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 2inb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/2inb ftp://data.pdbj.org/pub/pdb/validation_reports/in/2inb | HTTPS FTP |
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-Related structure data
Related structure data | 2nlvC 2nvmC 2nwvC 2okfC 3d7qC C: citing same article (ref.) |
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Similar structure data | |
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 SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 16120.028 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00107633.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 23125711 | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2 Details: 0.2M (NH4)2SO4, 10.0% Glycerol, 20.0% PEG-300, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9740, 0.9798, 0.9799 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.6→29.775 Å / Num. obs: 19879 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | 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: 1.6→29.775 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.642 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.082 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (4) RESIDUES OF A37 - A43 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS. THEY ARE UNMODELED. (5) RESIDUES OF A63 - A66 ARE DISORDERED AND ELECTRON DENSITIES ARE POOR.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.661 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.775 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.2296 Å / Origin y: 42.5928 Å / Origin z: 8.2214 Å
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Refinement TLS group | Selection: ALL |