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- PDB-7cnb: Crystal structure of Gp16 C-terminal domain from Bacillus virus phi29 -

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Basic information

Entry
Database: PDB / ID: 7cnb
TitleCrystal structure of Gp16 C-terminal domain from Bacillus virus phi29
ComponentsDNA packaging protein
KeywordsMOTOR PROTEIN / Crystal structure of Gp16 C-terminal domain from Bacillus virus phi29
Function / homology
Function and homology information


viral DNA genome packaging / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding
Similarity search - Function
Podovirus DNA packaging protein / Podovirus DNA encapsidation protein (Gp16) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA packaging protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsOuyang, S.Y. / Saeed, A.F.U.H.
CitationJournal: Biochemistry / Year: 2021
Title: Structural Insights into gp16 ATPase in the Bacteriophage φ29 DNA Packaging Motor.
Authors: Saeed, A.F.U.H. / Chan, C. / Guan, H. / Gong, B. / Guo, P. / Cheng, X. / Ouyang, S.
History
DepositionJul 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA packaging protein


Theoretical massNumber of molelcules
Total (without water)12,6751
Polymers12,6751
Non-polymers00
Water00
1
A: DNA packaging protein

A: DNA packaging protein


Theoretical massNumber of molelcules
Total (without water)25,3512
Polymers25,3512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.682, 42.682, 135.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein DNA packaging protein / Gp16 / ATPase gp16 / Gene product 16 / gp16 / Protein p16


Mass: 12675.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 16 / Production host: Escherichia coli (E. coli)
References: UniProt: P11014, 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.5, 1.8 M ammonium sulfate, 2% PEG monoethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.32→42.68 Å / Num. obs: 6004 / % possible obs: 100 % / Redundancy: 23.3 % / Biso Wilson estimate: 52.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.126 / Net I/σ(I): 17.8
Reflection shellResolution: 2.32→2.44 Å / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 835 / CC1/2: 0.883 / Rrim(I) all: 1.434 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimlessdata scaling
HKL-2000data collection
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→42.68 Å / Cor.coef. Fo:Fc: 0.932 / SU B: 8.761 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2708 --
Rwork0.2495 --
obs0.2495 5967 99.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.58 Å2 / Biso mean: 58.247 Å2 / Biso min: 30.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å2-0 Å2-0 Å2
2--1.04 Å2-0 Å2
3----2.08 Å2
Refinement stepCycle: final / Resolution: 2.32→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 0 0 881
Num. residues----107
LS refinement shellResolution: 2.32→2.379 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.291 426 -
obs--100 %

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