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Yorodumi- PDB-1j5s: Crystal structure of uronate isomerase (TM0064) from Thermotoga m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j5s | ||||||
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Title | Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution | ||||||
Components | URONATE ISOMERASE | ||||||
Keywords | ISOMERASE / TM0064 / URONATE ISOMERASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information glucuronate isomerase / glucuronate isomerase activity / D-galacturonate catabolic process / D-glucuronate catabolic process Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution. Authors: Schwarzenbacher, R. / Canaves, J.M. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshaghi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Guda, C. / Jaroszewski, ...Authors: Schwarzenbacher, R. / Canaves, J.M. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshaghi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Guda, C. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McMullan, D. / McPhillips, T.M. / Miller, M.A. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Robb, A. / Rodrigues, K. / Selby, T.L. / Spraggon, G. / Stevens, R.C. / Van Den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A. | ||||||
History |
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Remark 600 | HETEROGEN Residues H30, H32, W366, D397 coordinate a putative metal ion which has been modeled as ...HETEROGEN Residues H30, H32, W366, D397 coordinate a putative metal ion which has been modeled as water 1 (chain A), 2 (chain B) and 3 (chain C).' |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j5s.cif.gz | 272.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j5s.ent.gz | 226.4 KB | Display | PDB format |
PDBx/mmJSON format | 1j5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j5s ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j5s | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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-Components
#1: Protein | Mass: 53840.148 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0064 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXR9, glucuronate isomerase #2: Water | ChemComp-HOH / | |
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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: 2.81 Å3/Da / Density % sol: 55.94 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 6.8 Details: 50% (v/v) PEG-200, 0.1M Tris pH 7.0, pH 6.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 6.80 | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9184, 0.9794, 0.9792 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2002 | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.85→76.7 Å / Num. obs: 38502 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.36 Å2 / Rsym value: 0.075 / Net I/σ(I): 5.2 | ||||||||||||
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.232 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.85→24.99 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.831 / SU B: 21.087 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 Details: HOMOTRIMER, INVISIBLE SIDECHAIN IN RESIDUES 12,36,112,128,168,178,185,187,190,191,194,195,222, 223,257,258,398, UNACCOUNTED DENSITY NEXT TO M377 AND P344, UNACCOUNTED DENSITY NEXT TO R178.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.307 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→24.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.92 Å / Total num. of bins used: 20 /
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.233 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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