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- PDB-3c6h: Crystal Structure of the RB49 gp17 nuclease domain -

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Basic information

Entry
Database: PDB / ID: 3c6h
TitleCrystal Structure of the RB49 gp17 nuclease domain
ComponentsTerminase large subunit
KeywordsVIRAL PROTEIN / terminase nuclease
Function / homology
Function and homology information


viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #240 / Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesEnterobacteria phage RB49 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSun, S. / Rossmann, M.G.
CitationJournal: Cell / Year: 2008
Title: The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
Authors: Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao /
Abstract: Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The ...Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors.
History
DepositionFeb 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Terminase large subunit
B: Terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7334
Polymers52,6842
Non-polymers492
Water1,72996
1
A: Terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3662
Polymers26,3421
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3662
Polymers26,3421
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.436, 126.724, 52.391
Angle α, β, γ (deg.)90.000, 106.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Terminase large subunit


Mass: 26341.957 Da / Num. of mol.: 2 / Fragment: nuclease domain (UNP residues 359-564)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB49 (virus) / Gene: 17 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9T1C3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG400, 0.2M KCl, 50mM Tris pH 8.5, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 1, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 30585 / Num. obs: 29056 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.041 / Χ2: 1.665 / Net I/σ(I): 18.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 8.7 / Num. unique all: 2671 / Χ2: 1.195 / % possible all: 86.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.256 / Packing: 0.368
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral90.9 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C6A

3c6a


Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 704 4.8 %RANDOM
Rwork0.242 ---
obs0.242 13701 93.8 %-
all-14606 --
Solvent computationBsol: 63.631 Å2
Displacement parametersBiso mean: 53.643 Å2
Baniso -1Baniso -2Baniso -3
1-34.888 Å20 Å27.655 Å2
2---24.029 Å20 Å2
3----10.859 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 2 96 3099
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_scbond_it1.8722
X-RAY DIFFRACTIONc_mcangle_it2.7452
X-RAY DIFFRACTIONc_scangle_it2.9972.5
LS refinement shellResolution: 2.8→2.87 Å /
RfactorNum. reflection
Rfree0.387 40
Rwork0.332 -
obs-952
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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