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Yorodumi- PDB-1cgm: STRUCTURE DETERMINATION OF CUCUMBER GREEN MOTTLE MOSAIC VIRUS BY ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cgm | ||||||
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Title | STRUCTURE DETERMINATION OF CUCUMBER GREEN MOTTLE MOSAIC VIRUS BY X-RAY FIBER DIFFRACTION. SIGNIFICANCE FOR THE EVOLUTION OF TOBAMOVIRUSES | ||||||
Components |
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Keywords | VIRUS / Helical virus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cucumber green mottle mosaic virus | ||||||
Method | FIBER DIFFRACTION / Resolution: 3.4 Å | ||||||
Authors | Wang, H. / Stubbs, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Structure determination of cucumber green mottle mosaic virus by X-ray fiber diffraction. Significance for the evolution of tobamoviruses. Authors: Wang, H. / Stubbs, G. #1: Journal: Acta Crystallogr.,Sect.A / Year: 1993 Title: Molecular Dynamics in Refinement Against Fiber Diffraction Data Authors: Wang, H. / Stubbs, G. #2: Journal: Acta Crystallogr.,Sect.A / Year: 1990 Title: Fiber Diffraction Analysis of Cucumber Green Mottle Mosaic Virus Using Limited Numbers of Heavy-Atom Derivatives Authors: Lobert, S. / Stubbs, G. #3: Journal: Acta Crystallogr.,Sect.A / Year: 1989 Title: The Probability Distributions of X-Ray Intensities in Fiber Diffraction: Largest Likely Values for Fiber Diffraction R Factors Authors: Stubbs, G. #4: Journal: Acta Crystallogr.,Sect.A / Year: 1987 Title: Isomorphous Replacement in Fiber Diffraction Using Limited Numbers of Heavy-Atom Derivatives Authors: Namba, K. / Stubbs, G. #5: Journal: Acta Crystallogr.,Sect.A / Year: 1985 Title: Solving the Phase Problem in Fiber Diffraction. Application to Tobacco Mosaic Virus at 3.6 Angstroms Resolution Authors: Namba, K. / Stubbs, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cgm.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cgm.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 1cgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cgm_validation.pdf.gz | 362.9 KB | Display | wwPDB validaton report |
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Full document | 1cgm_full_validation.pdf.gz | 375.6 KB | Display | |
Data in XML | 1cgm_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1cgm_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/1cgm ftp://data.pdbj.org/pub/pdb/validation_reports/cg/1cgm | 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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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: ASN E 3 - PRO E 4 OMEGA =147.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: LEU E 51 - PRO E 52 OMEGA =134.87 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ASN E 101 - PRO E 102 OMEGA =299.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 49 / Num. of operations: 49 / Rise per n subunits: 70.8 Å / Rotation per n subunits: 1080 °) | ||||||||
Details | THE FOLLOWING TRANSFORMATION REPRESENTS HELICAL SYMMETRY WITH THE HELIX AXIS ON THE Z AXIS. APPLYING THIS TRANSFORMATION 48 TIMES TO THE COORDINATES IN THIS ENTRY WILL YIELD 49 SUBUNITS IN THREE TURNS OF THE HELIX. THE FULL (49 SUBUNIT) HELICAL REPEAT IS 70.8 ANGSTROMS LONG IN THE Z DIRECTION. MTRIX1 0.926900 -0.375300 0.000000 0.00000 MTRIX2 0.375300 0.926900 0.000000 0.00000 MTRIX3 0.000000 0.000000 1.000000 1.44490 THE LENGTH OF THE BASIC REPEAT UNIT IS 70.8 ANGSTROMS. THE NUMBER OF SUBUNITS IN THE BASIC REPEAT UNIT IS 49. |
-Components
#1: RNA chain | Mass: 958.660 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 17303.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cucumber green mottle mosaic virus / Tissue: WATERMELON / References: UniProt: P19521, UniProt: P69475*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: FIBER DIFFRACTION |
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-Data collection
Radiation wavelength | Relative weight: 1 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.093 / Rfactor obs: 0.093 / Highest resolution: 3.4 Å Details: STRUCTURE WAS DETERMINED FROM FIBER DIFFRACTION DATA BY MULTI-DIMENSIONAL ISOMORPHOUS REPLACEMENT WITH THREE HEAVY ATOM DERIVATIVES. CGMMV HAS 36 PERCENT SEQUENCE HOMOLOGY WITH TOBACCO ...Details: STRUCTURE WAS DETERMINED FROM FIBER DIFFRACTION DATA BY MULTI-DIMENSIONAL ISOMORPHOUS REPLACEMENT WITH THREE HEAVY ATOM DERIVATIVES. CGMMV HAS 36 PERCENT SEQUENCE HOMOLOGY WITH TOBACCO MOSAIC VIRUS (TMV). THE STRUCTURE INCLUDES ALL 160 AMINO ACIDS, 3 RNA NUCLEOTIDES (MODELED AS GAA) AND 6 WATER MOLECULES. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.4 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor obs: 0.093 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.7 |