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- PDB-1una: UNASSEMBLED VIRUS COAT PROTEIN DIMER, BACTERIOPHAGE RNA-BINDING DIMER -

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Basic information

Entry
Database: PDB / ID: 1una
TitleUNASSEMBLED VIRUS COAT PROTEIN DIMER, BACTERIOPHAGE RNA-BINDING DIMER
ComponentsGA UNASSEMBLED COAT PROTEIN DIMER
KeywordsVIRAL PROTEIN / UNASSEMBLED VIRUS COAT PROTEIN DIMER / BACTERIOPHAGE / RNA-BINDING DIMER / TRANSLATIONAL REPRESSOR
Function / homology
Function and homology information


T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage GA (virus)
MethodX-RAY DIFFRACTION / MOL. REPLACEMENT / Resolution: 2.8 Å
AuthorsNi, C.-Z. / Ely, K.R.
CitationJournal: Protein Sci. / Year: 1996
Title: Crystal structure of the coat protein from the GA bacteriophage: model of the unassembled dimer.
Authors: Ni, C.Z. / White, C.A. / Mitchell, R.S. / Wickersham, J. / Kodandapani, R. / Peabody, D.S. / Ely, K.R.
History
DepositionApr 25, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GA UNASSEMBLED COAT PROTEIN DIMER
B: GA UNASSEMBLED COAT PROTEIN DIMER


Theoretical massNumber of molelcules
Total (without water)27,2932
Polymers27,2932
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-50 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.300, 60.500, 67.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GA UNASSEMBLED COAT PROTEIN DIMER / TRANSLATIONAL REPRESSOR


Mass: 13646.364 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THIS BACTERIOPHAGE COAT PROTEIN WAS CRYSTALLIZED AS AN UNASSEMBLED DIMER. IT DID NOT FORM VIRAL CAPSIDS.
Source: (gene. exp.) Enterobacteria phage GA (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage BZ13
Description: GA COAT SEQUENCE WAS CLONED FROM RNA ISOLATED FROM GA BACTERIOPHAGE PROVIDED BY DR. A. HIRASHIMA, KEIO UNIVERSITY. THE COAT GENE IN THIS DIFFERS AT FOUR SITES FROM THE WIDETYPE PUBLISHED ...Description: GA COAT SEQUENCE WAS CLONED FROM RNA ISOLATED FROM GA BACTERIOPHAGE PROVIDED BY DR. A. HIRASHIMA, KEIO UNIVERSITY. THE COAT GENE IN THIS DIFFERS AT FOUR SITES FROM THE WIDETYPE PUBLISHED SEQUENCE (INOKUCHI ET AL.,(1986) J. BIOCHEM. 99\: 1169)
Gene: GA COAT GENE / Plasmid: PUC118 / Gene (production host): GA COAT GENE / Production host: Escherichia coli (E. coli) / Strain (production host): CSH41F- / References: UniProt: P07234

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 46 %
Crystal grow
*PLUS
Temperature: 13 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlGA dimers1drop
25 mMTris-HCl1drop
350 mM1dropNaCl
40.1 MTris-maleate1reservoir
5PEG10001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 3, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→55 Å / Num. obs: 10793 / % possible obs: 94 % / Redundancy: 3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 5 / % possible all: 81
Reflection
*PLUS
Lowest resolution: 4.79 Å / Num. obs: 6248 / Num. measured all: 32352 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 3.02 Å / Num. unique obs: 1157 / Num. measured obs: 3616 / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 6.3

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Processing

Software
NameVersionClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLORphasing
RefinementMethod to determine structure: MOL. REPLACEMENT
Starting model: MS2 COAT PROTEIN DIMER (1MS2)

1ms2
PDB Unreleased entry


Resolution: 2.8→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.284 -10 %
Rwork0.204 --
obs-5372 50 %
Displacement parametersBiso mean: 17.13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 0 0 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0310.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0130.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it6.9581.75
X-RAY DIFFRACTIONp_mcangle_it9.6492.5
X-RAY DIFFRACTIONp_scbond_it7.7771.75
X-RAY DIFFRACTIONp_scangle_it10.1312.5
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1920.3
X-RAY DIFFRACTIONp_multtor_nbd0.2110.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1660.3
X-RAY DIFFRACTIONp_planar_tor1.55
X-RAY DIFFRACTIONp_staggered_tor22.520
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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