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Yorodumi- PDB-1yac: THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE YCAC GENE PRODUCT FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yac | ||||||
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Title | THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE YCAC GENE PRODUCT FROM ESCHERICHIA COLI REVEALS AN OCTAMERIC HYDROLASE OF UNKNOWN SPECIFICITY | ||||||
Components | YCAC GENE PRODUCT | ||||||
Keywords | UNKNOWN BACTERIAL HYDROLASE / THREE LAYER ALPHA-BETA-ALPHA SANDWICH TOPOLOGY / ENTB HOMOLOG / CSHASE HOMOLOG | ||||||
Function / homology | Function and homology information Lyases / hydrolase activity / lyase activity / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Colovos, C. / Cascio, D. / Yeates, T.O. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The 1.8 A crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity. Authors: Colovos, C. / Cascio, D. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yac.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yac.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 1yac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yac_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 1yac_full_validation.pdf.gz | 431.3 KB | Display | |
Data in XML | 1yac_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1yac_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/1yac ftp://data.pdbj.org/pub/pdb/validation_reports/ya/1yac | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.151263, 0.988474, -0.00626), Vector: |
-Components
#1: Protein | Mass: 22978.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YCAC / References: UniProt: P21367 #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: 2.57 Å3/Da / Density % sol: 41 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 |
Detector | Type: ADSC / Detector: CCD / Date: Jul 9, 1997 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 45552 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.39 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.64 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.56 / % possible all: 97.6 |
Reflection | *PLUS Num. obs: 45076 / % possible obs: 98.8 % / Num. measured all: 308775 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 95.6 % / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→8 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.2187 |