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- PDB-3rlc: Crystal structure of the read-through domain from bacteriophage Q... -

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Basic information

Entry
Database: PDB / ID: 3rlc
TitleCrystal structure of the read-through domain from bacteriophage Qbeta A1 protein, hexagonal crystal form
ComponentsA1 protein
KeywordsSTRUCTURAL PROTEIN / Beta-barrel / polyproline helix
Function / homologyRead-through domain / Read-through domain / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / viral capsid / structural molecule activity / Minor capsid protein A1
Function and homology information
Biological speciesEnterobacteria phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsRumnieks, J. / Tars, K.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of the read-through domain from bacteriophage Qbeta A1 protein
Authors: Rumnieks, J. / Tars, K.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _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

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Assembly

Deposited unit
A: A1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5725
Polymers21,7951
Non-polymers7774
Water36020
1
A: A1 protein
hetero molecules

A: A1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,14310
Polymers43,5892
Non-polymers1,5548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3450 Å2
ΔGint9 kcal/mol
Surface area17500 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.110, 69.110, 167.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein A1 protein / A1 read-through protein


Mass: 21794.596 Da / Num. of mol.: 1 / Fragment: Read-through domain, UNP residues 145-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Gene: A1 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8LTE1
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40% PEG 300, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03874 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03874 Å / Relative weight: 1
ReflectionResolution: 2.9→34.555 Å / Num. obs: 5773 / % possible obs: 100 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 9.5 % / Rsym value: 0.098 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.9-3.06100.5431.479417960.543100
3.06-3.249.90.2922.676357710.292100
3.24-3.479.80.196471557310.196100
3.47-3.749.80.1226.266596790.122100
3.74-4.19.70.0829.261096330.082100
4.1-4.599.50.06111.955375810.061100
4.59-5.299.50.0611.549275210.06100
5.29-6.489.10.0778.241114520.077100
6.48-9.178.60.03716.831943710.037100
9.17-34.5557.30.02918.817262380.02998.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.96 Å40.8 Å
Translation2.96 Å40.8 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.93 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2542 / WRfactor Rwork: 0.1817 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7806 / SU B: 18.817 / SU ML: 0.355 / SU Rfree: 0.4537 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2969 263 4.6 %RANDOM
Rwork0.2128 ---
obs0.2166 5728 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.75 Å2 / Biso mean: 41.5926 Å2 / Biso min: 16.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20.87 Å20 Å2
2--1.74 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 35 20 1466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221487
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9712011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09423.08868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39715224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4591511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221146
X-RAY DIFFRACTIONr_mcbond_it0.5841.5883
X-RAY DIFFRACTIONr_mcangle_it1.14621432
X-RAY DIFFRACTIONr_scbond_it1.6093604
X-RAY DIFFRACTIONr_scangle_it2.8884.5579
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 16 -
Rwork0.303 383 -
all-399 -
obs--100 %

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