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Yorodumi- PDB-1dw9: Structure of cyanase reveals that a novel dimeric and decameric a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dw9 | ||||||
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Title | Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site | ||||||
Components | CYANATE LYASE | ||||||
Keywords | LYASE / CYANATE DEGRADATION / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG | ||||||
Function / homology | Function and homology information cyanate catabolic process / cyanase / cyanate hydratase activity / DNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Walsh, M.A. / Otwinowski, Z. / Perrakis, A. / Anderson, P.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Structure / Year: 2000 Title: Structure of Cyanase Reveals that a Novel Dimeric and Decameric Arrangement of Subunits is Required for Formation of the Enzyme Active Site Authors: Walsh, M.A. / Otwinowski, Z. / Perrakis, A. / Anderson, P.M. / Joachimiak, A. #1: Journal: J.Bacteriol. / Year: 1987 Title: Characterization of High-Level Expression and Sequencing of the Escherichia Coli K-12 Cyns Gene Encoding Cyanase Authors: Sung, Y. / Anderson, P.M. / Fuchs, J.A. #2: Journal: Biochemistry / Year: 1986 Title: Kinetic Properties of Cyanase Authors: Anderson, P.M. / Little, R.M. #3: Journal: Biochemistry / Year: 1986 Title: Interaction of Mono- and Dianions with Cyanase: Evidence for Apparent Half-Site Binding Authors: Anderson, P.M. / Johnson, W.V. / Endrizzi, J.A. / Little, R.M. / Korte, J.J. #4: Journal: Biochemistry / Year: 1980 Title: Purification and Properties of the Inducible Enzyme Cyanase Authors: Anderson, P.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEET STRUCTURE OF THIS ASSEMBLY IS COMPRISED OF FIVE SHEETS ... SHEET DETERMINATION METHOD: DSSP THE SHEET STRUCTURE OF THIS ASSEMBLY IS COMPRISED OF FIVE SHEETS THAT FORM AN EQUATORIAL GIRDLE AROUND THE DECAMERIC ASSEMBLY. EACH SHEET IS MADE UP OF FOUR STRANDS FROM TWO PROTEIN CHAINS EACH CONTRIBUTING TWO STRANDS |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dw9.cif.gz | 346 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dw9.ent.gz | 294.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dw9_validation.pdf.gz | 528.6 KB | Display | wwPDB validaton report |
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Full document | 1dw9_full_validation.pdf.gz | 574 KB | Display | |
Data in XML | 1dw9_validation.xml.gz | 85.1 KB | Display | |
Data in CIF | 1dw9_validation.cif.gz | 118.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/1dw9 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/1dw9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17255.377 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00816, EC: 4.3.99.1 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / #4: 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: 2.53 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.3 Details: SELENOMETHIONINE LABELLED CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF ...Details: SELENOMETHIONINE LABELLED CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF 50 MM TRIC/HCL, PH =7.3. MICROSEEDING WITH WILD-TYPE CRYSTALS PRODUCED CRYSTALS THAT GREW TO 0.1 X 0.2 X 0.7 MM OVER 5-7 DAYS. | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 51 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting drop / Details: used microseeding | ||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.9465, 0.9793, 0.9795, 1.033, 1.078, 1.00 | |||||||||||||||||||||
Detector | Type: ARGONNE APS-1 / Detector: CCD / Date: Jul 15, 1998 / Details: MIRROR | |||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→20 Å / Num. obs: 187107 / % possible obs: 94.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.039 / Net I/σ(I): 26.4 | |||||||||||||||||||||
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.198 / % possible all: 80.6 | |||||||||||||||||||||
Reflection | *PLUS Num. measured all: 524489 / Rmerge(I) obs: 0.039 | |||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 80.6 % / Rmerge(I) obs: 0.198 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→20 Å / SU B: 1.66 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.092 Details: NCS RESTRAINTS NOT EMPLOYED ALTERNATIVE CONFORMATIONS WERE MODELLED FOR THE FOLLOWING AMINO ACID SIDE CHAINS CHAIN A: 25 27 31 34 66 78 101 128 132 133 CHAIN B: 10 27 60 66 78 101 128 131 ...Details: NCS RESTRAINTS NOT EMPLOYED ALTERNATIVE CONFORMATIONS WERE MODELLED FOR THE FOLLOWING AMINO ACID SIDE CHAINS CHAIN A: 25 27 31 34 66 78 101 128 132 133 CHAIN B: 10 27 60 66 78 101 128 131 CHAIN C: 27 40 60 78 88 101 128 132 CHAIN D: 27 78 101 128 133 CHAIN E: 27 31 34 40 78 101 128 CHAIN F: 40 60 78 101 128 CHAIN G: 25 27 34 78 101 128 CHAIN H: 31 40 78 101 128 CHAIN I: 27 60 101 128 CHAIN J: 27 31 78 101 128 THIS STRUCTURE WAS DETERMINED AS PART OF THE STRUCTURAL GENOMICS INITIATIVE AT ARGONNE NATIONAL LABORATORY
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Displacement parameters | Biso mean: 17.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.15 / Rfactor Rwork: 0.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |