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- PDB-1msc: CRYSTAL STRUCTURE OF MS2 COAT PROTEIN DIMER -

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Basic information

Entry
Database: PDB / ID: 1msc
TitleCRYSTAL STRUCTURE OF MS2 COAT PROTEIN DIMER
ComponentsBACTERIOPHAGE MS2 COAT PROTEIN
KeywordsVIRAL PROTEIN / TRANSLATION REPRESSOR
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein 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 speciesEnterobacterio phage MS2 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsNi, C.-Z. / Kodandapani, R. / Ely, K.R.
Citation
Journal: Structure / Year: 1995
Title: Crystal structure of the MS2 coat protein dimer: implications for RNA binding and virus assembly.
Authors: Ni, C.Z. / Syed, R. / Kodandapani, R. / Wickersham, J. / Peabody, D.S. / Ely, K.R.
#1: Journal: Protein Sci. / Year: 1995
Title: Crystallization of the MS2 Translational Repressor Alone and Complexed to Bromouridine
Authors: Ni, C.-Z. / Hettinga, B.S. / Wickersham, J. / Mitchell, R.S. / Williamson, M.M. / Celikel, R. / Prange, T. / Fourme, R. / Krapcho, K.J. / Thulin, C. / Talbot, P. / Gesteland, R.F. / Ely, K.R.
History
DepositionApr 28, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Assembly

Deposited unit
A: BACTERIOPHAGE MS2 COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,7091
Polymers13,7091
Non-polymers00
Water2,000111
1
A: BACTERIOPHAGE MS2 COAT PROTEIN

A: BACTERIOPHAGE MS2 COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,4192
Polymers27,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6940 Å2
ΔGint-48 kcal/mol
Surface area12510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.200, 55.700, 28.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BACTERIOPHAGE MS2 COAT PROTEIN


Mass: 13709.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage MS2Bacteriophage MS2 / Gene: MS2 COAT GENE / Gene (production host): MS2 COAT GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P03612
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growDetails: COMPND MOLECULE: MS2 UNASSEMBLED COAT PROTEIN DIMER. THIS BACTERIOPHAGE COAT PROTEIN WAS CRYSTALLIZED AS AN UNASSEMBLED DIMER; IT DID NOT FORM VIRAL CAPSIDS.
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG80001drop
23 mg/mlprotein1drop
3100 mMcitrate-phosphate1reservoir

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Data collection

DetectorDate: Dec 7, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.03→55 Å / Num. obs: 7447 / % possible obs: 90 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.031
Reflection
*PLUS
Num. measured all: 23935 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 2.19 Å / % possible obs: 65 % / Num. unique obs: 1033 / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
PROLSQrefinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
RefinementResolution: 2→8 Å / σ(F): 3 /
RfactorNum. reflection% reflection
obs0.2 6668 90 %
Displacement parametersBiso mean: 34.47 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 0 111 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0660.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.2390.3
X-RAY DIFFRACTIONp_multtor_nbd0.2920.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2870.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.85
X-RAY DIFFRACTIONp_staggered_tor24.120
X-RAY DIFFRACTIONp_orthonormal_tor42.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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