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- PDB-7lw0: Structural and Biochemical Insight into Assembly of Molecular Mot... -

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Basic information

Entry
Database: PDB / ID: 7lw0
TitleStructural and Biochemical Insight into Assembly of Molecular Motors Involved in Viral DNA Packaging
ComponentsTerminase small subunit
KeywordsVIRAL PROTEIN / DNA Packaging / Terminase
Function / homology
Function and homology information


viral terminase, small subunit / sequence-specific DNA binding, bending / viral DNA genome packaging / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / ATP hydrolysis activity / ATP binding
Similarity search - Function
Bacteriophage lambda, Nu1, terminase small subunit / Phage DNA packaging protein Nu1 / Putative DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Terminase small subunit
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsOrtega, M.E.
CitationJournal: To Be Published
Title: Structural and Biochemical Insight into Assembly of Molecular Motors Involved in Viral DNA Packaging
Authors: Ortega, M.E. / Randriamihaja, A. / Rossen, N. / Brannon, J.P. / Marquez, C. / West, R. / Dabbagh, S. / Robles, R. / LeGue, A.
History
DepositionFeb 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminase small subunit
B: Terminase small subunit
C: Terminase small subunit
D: Terminase small subunit
E: Terminase small subunit
F: Terminase small subunit
G: Terminase small subunit
H: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)50,1138
Polymers50,1138
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-35 kcal/mol
Surface area23560 Å2
Unit cell
Length a, b, c (Å)41.748, 42.772, 57.222
Angle α, β, γ (deg.)89.980, 89.980, 89.880
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Terminase small subunit / DNA-packaging protein Nu1 / Gene product Nu1 / gpNu1


Mass: 6264.111 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: Nu1, lambdap01 / Production host: Escherichia coli (E. coli)
References: UniProt: P03707, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: isopropanol 5%, 10mM magnesium acetate, tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.32→34.3 Å / Num. obs: 16731 / % possible obs: 97.5 % / Redundancy: 2.6 % / CC1/2: 0.96 / Net I/σ(I): 11.5
Reflection shellResolution: 2.32→2.4 Å / Num. unique obs: 1681 / CC1/2: 0.976

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→34.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.457 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.609 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1517 1673 10 %RANDOM
Rwork0.1189 ---
obs0.1222 15058 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.45 Å2 / Biso mean: 25.537 Å2 / Biso min: 9.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.07 Å2
2---0.09 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.32→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 0 0 3504
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133560
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183312
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6324784
X-RAY DIFFRACTIONr_angle_other_deg1.3171.5917672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10223.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.67115640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5451524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02752
LS refinement shellResolution: 2.32→2.376 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.15 108 -
Rwork0.081 1060 -
obs--90.54 %

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