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Yorodumi- PDB-2isb: Crystal structure of Fumarase of FUM-1 (NP_069927.1) from Archaeo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2isb | |||||||||
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Title | Crystal structure of Fumarase of FUM-1 (NP_069927.1) from Archaeoglobus Fulgidus at 1.66 A resolution | |||||||||
Components | Fumarase | |||||||||
Keywords | LYASE / NP_069927.1 / Fumarase of FUM-1 / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG | |||||||||
Function / homology | fumarase / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily / Fumarase C-terminus / hydro-lyase activity / Alpha-Beta Barrel / Alpha Beta / Fumarase (Fum-1) Function and homology information | |||||||||
Biological species | Archaeoglobus fulgidus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: To be published Title: Crystal structure of Fumarase of FUM-1 (NP_069927.1) from Archaeoglobus Fulgidus at 1.66 A resolution Authors: Joint Center for Structural Genomics (JCSG) | |||||||||
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 WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2isb.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2isb.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 2isb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2isb ftp://data.pdbj.org/pub/pdb/validation_reports/is/2isb | 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: 21882.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: FUM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O29167, fumarate hydratase |
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#2: 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: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.8 Details: 0.2M Li Acetate, 20.0% PEG-3350, No Buffer, pH 7.8, 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: 8.2.1 / Wavelength: 1.00000, 0.97966, 0.97950 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.66→21.152 Å / Num. obs: 25660 / % possible obs: 97.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 5.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.66→21.152 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.292 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3. DENSITY IS WEAK FOR THE FOLLOWING REGIONS: A-3 - 1, A70 - 73.
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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: 16.333 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→21.152 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 41.8297 Å / Origin y: 28.2611 Å / Origin z: 12.9866 Å
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Refinement TLS group | Selection: ALL |