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

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Basic information

Entry
Database: PDB / ID: 7lxs
TitleStructural and Biochemical Insight into Assembly of Molecular Motors Involved in Viral DNA Packaging
ComponentsTerminase, small subunit
KeywordsVIRAL PROTEIN / DNA Packaging / Terminase
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesBacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 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
DepositionMar 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)47,0298
Polymers47,0298
Non-polymers00
Water00
1
A: Terminase, small subunit
C: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area5520 Å2
MethodPISA
2
B: Terminase, small subunit

D: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1140 Å2
ΔGint-12 kcal/mol
Surface area5570 Å2
MethodPISA
3
E: Terminase, small subunit
H: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-12 kcal/mol
Surface area5540 Å2
MethodPISA
4
F: Terminase, small subunit

G: Terminase, small subunit


Theoretical massNumber of molelcules
Total (without water)11,7572
Polymers11,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1140 Å2
ΔGint-12 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.747, 50.761, 68.527
Angle α, β, γ (deg.)90.000, 88.360, 90.110
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Terminase, small subunit


Mass: 5878.606 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Escherichia coli (E. coli)

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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: 1.83 Å3/Da / Density % sol: 32.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 50mM MES pH 6.5, 10mM zinc chloride, 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.206→24.74 Å / Num. obs: 15881 / % possible obs: 95.1 % / Redundancy: 3.7 % / CC1/2: 0.999 / Net I/σ(I): 93.9
Reflection shellResolution: 2.21→2.29 Å / Num. unique obs: 1287 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LW0

7lw0


Resolution: 2.21→24.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.009 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.142 1605 10.1 %RANDOM
Rwork0.1398 ---
obs0.14 14295 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.92 Å2 / Biso mean: 18.288 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.03 Å2-0.01 Å2
2---0.03 Å2-0.02 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.21→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 0 0 3296
Num. residues----440
LS refinement shellResolution: 2.21→2.263 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.254 93 -
Rwork0.253 900 -
obs--78.19 %

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