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- PDB-1rmv: RIBGRASS MOSAIC VIRUS, FIBER DIFFRACTION -

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Basic information

Entry
Database: PDB / ID: 1rmv
TitleRIBGRASS MOSAIC VIRUS, FIBER DIFFRACTION
Components
  • RIBGRASS MOSAIC VIRUS COAT PROTEIN
  • RIBGRASS MOSAIC VIRUS RNA
KeywordsVirus/RNA / RIBGRASS MOSAIC VIRUS / TOBAMOVIRUS / RMV CLUSTER / COAT PROTEIN (VIRAL) / COMPLEX (COAT PROTEIN-RNA) / Helical virus / Virus-RNA COMPLEX
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
Similarity search - Component
Biological speciesRibgrass mosaic virus
MethodFIBER DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, H. / Stubbs, G.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1993
Title: Molecular dynamics in refinement against fiber diffraction data.
Authors: Wang, H. / Stubbs, G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary X-Ray Diffraction Studies of Ribgrass Mosaic Virus
Authors: Wang, H. / Planchart, A. / Allen, D. / Pattanayek, R. / Stubbs, G.
#2: 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
DepositionFeb 11, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RIBGRASS MOSAIC VIRUS RNA
A: RIBGRASS MOSAIC VIRUS COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,5112
Polymers18,5112
Non-polymers00
Water00
1
B: RIBGRASS MOSAIC VIRUS RNA
A: RIBGRASS MOSAIC VIRUS COAT PROTEIN
x 49


Theoretical massNumber of molelcules
Total (without water)907,04598
Polymers907,04598
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation48
identity operation1_555x,y,z1
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
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, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 49 / Num. of operations: 49 / Rise per n subunits: 69.7 Å / Rotation per n subunits: 1080 °)
DetailsTHE BASIC REPEAT UNIT OF THE VIRAL HELIX IS 69.7 ANGSTROMS IN LENGTH WITH 49 SUBUNITS IN 3 HELICAL TURNS.

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Components

#1: RNA chain RIBGRASS MOSAIC VIRUS RNA


Mass: 958.660 Da / Num. of mol.: 1 / Fragment: GAA / Source method: isolated from a natural source / Source: (natural) Ribgrass mosaic virus / Genus: Tobamovirus
#2: Protein RIBGRASS MOSAIC VIRUS COAT PROTEIN


Mass: 17552.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ribgrass mosaic virus / Genus: Tobamovirus / References: UniProt: P03580
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Sample preparation

Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOT GX-6 / Wavelength: 1.5418
DetectorType: KODAK FILM / Detector: FILM / Date: Oct 1, 1990 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 6045 / % possible obs: 91.2 % / Redundancy: 4 %

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Processing

Software
NameClassification
FXPLORrefinement
RADPVdata reduction
SCALVdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TMV

2tmv


Resolution: 2.9→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.095 --
obs-5315 91.2 %
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 67 0 0 1302
Software
*PLUS
Name: FXPLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.095
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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