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Yorodumi- PDB-1gca: THE 1.7 ANGSTROMS REFINED X-RAY STRUCTURE OF THE PERIPLASMIC GLUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gca | ||||||
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Title | THE 1.7 ANGSTROMS REFINED X-RAY STRUCTURE OF THE PERIPLASMIC GLUCOSE(SLASH)GALACTOSE RECEPTOR FROM SALMONELLA TYPHIMURIUM | ||||||
Components | GLUCOSE/GALACTOSE-BINDING PROTEIN | ||||||
Keywords | GALACTOSE-BINDING PROTEIN | ||||||
Function / homology | Function and homology information : / chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Zou, J.-Y. / Mowbray, S.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: The 1.7 A refined X-ray structure of the periplasmic glucose/galactose receptor from Salmonella typhimurium. Authors: Zou, J.Y. / Flocco, M.M. / Mowbray, S.L. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Ribose and Glucose-Galactose Receptors. Competitors in Bacterial Chemotaxis Authors: Mowbray, S.L. #2: Journal: Receptor / Year: 1990 Title: Structure of the Periplasmic Glucose(Slash)Galactose Receptor of Salmonella Typhimurium Authors: Mowbray, S.L. / Smith, R.D. / Cole, L.B. #3: Journal: J.Mol.Biol. / Year: 1981 Title: Preliminary X-Ray Data for the Galactose Binding Protein from Salmonella Typhimurium Authors: Alber, T. / Fahnestock, M. / Mowbray, S. / Petsko, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gca.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gca.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gca_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 1gca_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 1gca_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1gca_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gca ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gca | 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
#1: Protein | Mass: 33460.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P23905 |
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#2: Sugar | ChemComp-GAL / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SEE REFERENCE 1. SWISS- ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | *PLUS Method: vapor diffusion / Details: Mowbray, S.L., (1990) Receptor, 1, 41. |
Components of the solutions | *PLUS Conc.: 15 % / Common name: PEG4000 |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 9999 Å / Num. obs: 34605 / Num. measured all: 63576 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / % possible obs: 78.6 % / Num. unique obs: 6070 / Num. measured obs: 8119 / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 18.2 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.19 / Highest resolution: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.77 Å / Lowest resolution: 7.5 Å / Num. reflection obs: 28224 / σ(I): 1 / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.67 |