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- PDB-2qud: PP7 Coat Protein Dimer -

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Basic information

Entry
Database: PDB / ID: 2qud
TitlePP7 Coat Protein Dimer
ComponentsCoat protein
KeywordsRNA BINDING PROTEIN / Bacteriophage / RNA-Protein Complex / Capsid protein
Function / homology
Function and homology information


T=3 icosahedral viral capsid / regulation of translation / RNA binding / identical protein binding
Similarity search - Function
Bacteriophage PP7, coat / Phage PP7 coat protein / MS2 Viral Coat Protein / MS2 Viral Coat Protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas phage PP7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChao, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for the coevolution of a viral RNA-protein complex.
Authors: Chao, J.A. / Patskovsky, Y. / Almo, S.C. / Singer, R.H.
History
DepositionAug 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3253
Polymers27,2332
Non-polymers921
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.985, 154.985, 31.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Coat protein


Mass: 13616.476 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage PP7 (virus) / Genus: Levivirus / Gene: PP7 Coat Protein / Plasmid: pET22HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q38062
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M Na Malonat, 0.1M HEPES, 0.5% Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2006 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 37546 / Num. obs: 37546 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 36.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3737 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DWN

1dwn


Resolution: 1.6→38.75 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1876 -5.0%
Rwork0.157 ---
all0.159 35670 --
obs0.159 35767 99.73 %-
Refinement stepCycle: LAST / Resolution: 1.6→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 6 352 2222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.512

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