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- PDB-1cgm: STRUCTURE DETERMINATION OF CUCUMBER GREEN MOTTLE MOSAIC VIRUS BY ... -

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Basic information

Entry
Database: PDB / ID: 1cgm
TitleSTRUCTURE DETERMINATION OF CUCUMBER GREEN MOTTLE MOSAIC VIRUS BY X-RAY FIBER DIFFRACTION. SIGNIFICANCE FOR THE EVOLUTION OF TOBAMOVIRUSES
Components
  • CUCUMBER GREEN MOTTLE MOSAIC VIRUS
  • RNA (5'-R(P*GP*AP*A)-3')
KeywordsVIRUS / Helical virus
Function / homology
Function and homology information


helical viral capsid / structural molecule activity
Similarity search - Function
Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / Capsid protein / Capsid protein
Similarity search - Component
Biological speciesCucumber green mottle mosaic virus
MethodFIBER DIFFRACTION / Resolution: 3.4 Å
AuthorsWang, 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
DepositionNov 17, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: RNA (5'-R(P*GP*AP*A)-3')
E: CUCUMBER GREEN MOTTLE MOSAIC VIRUS


Theoretical massNumber of molelcules
Total (without water)18,2622
Polymers18,2622
Non-polymers00
Water905
1
I: RNA (5'-R(P*GP*AP*A)-3')
E: CUCUMBER GREEN MOTTLE MOSAIC VIRUS
x 49


Theoretical massNumber of molelcules
Total (without water)894,83298
Polymers894,83298
Non-polymers00
Water88349
TypeNameSymmetry operationNumber
helical symmetry operation48
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)1.000, 1.000, 70.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
Atom site foot note1: 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
SymmetryHelical 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 °)
DetailsTHE 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.

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Components

#1: RNA chain RNA (5'-R(P*GP*AP*A)-3')


Mass: 958.660 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein CUCUMBER GREEN MOTTLE MOSAIC VIRUS


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 / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Data collection

Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor 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 stepCycle: LAST / Highest resolution: 3.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 67 0 5 1296
Refine LS restraints
Refine-IDTypeDev ideal
FIBER DIFFRACTIONx_bond_d0.016
FIBER DIFFRACTIONx_bond_d_na
FIBER DIFFRACTIONx_bond_d_prot
FIBER DIFFRACTIONx_angle_d
FIBER DIFFRACTIONx_angle_d_na
FIBER DIFFRACTIONx_angle_d_prot
FIBER DIFFRACTIONx_angle_deg3.7
FIBER DIFFRACTIONx_angle_deg_na
FIBER DIFFRACTIONx_angle_deg_prot
FIBER DIFFRACTIONx_dihedral_angle_d
FIBER DIFFRACTIONx_dihedral_angle_d_na
FIBER DIFFRACTIONx_dihedral_angle_d_prot
FIBER DIFFRACTIONx_improper_angle_d
FIBER DIFFRACTIONx_improper_angle_d_na
FIBER DIFFRACTIONx_improper_angle_d_prot
FIBER DIFFRACTIONx_mcbond_it
FIBER DIFFRACTIONx_mcangle_it
FIBER DIFFRACTIONx_scbond_it
FIBER DIFFRACTIONx_scangle_it
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

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