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- PDB-2o0h: T4 gp17 ATPase domain mutant complexed with ATP -

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Basic information

Entry
Database: PDB / ID: 2o0h
TitleT4 gp17 ATPase domain mutant complexed with ATP
ComponentsDNA packaging protein Gp17Chromosome
KeywordsHYDROLASE / nucleotide-binding fold
Function / homology
Function and homology information


viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / 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 ...viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / 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
Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Terminase, large subunit
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.88 Å
AuthorsSun, S. / Rossmann, M.G.
CitationJournal: MOL.CELL / Year: 2007
Title: The Structure of the ATPase that Powers DNA Packaging into Bacteriophage T4 Procapsids
Authors: Sun, S. / Kondabagil, K. / Gentz, P.M. / Rossmann, M.G. / Rao, V.B.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA packaging protein Gp17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7322
Polymers44,2251
Non-polymers5071
Water8,107450
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.213, 62.261, 126.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsEach asymmetric unit contains one copy of gp17 ATPase domain. The stoichiometry of gp17 in T4 prohead is unknown.

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Components

#1: Protein DNA packaging protein Gp17 / Chromosome / Terminase


Mass: 44225.098 Da / Num. of mol.: 1 / Fragment: N-terminal ATPase domain / Mutation: D255E, E256D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 17 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3(pLys) / References: UniProt: P17312
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 3350, 0.2M KNO3, 8% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.20373
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2006
Details: Si(111) Double Crystal Monochromator. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.20373 Å / Relative weight: 1
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
6.917.5539730.1582.213.3776699.9
3.7222.11084680.0431.9122939587.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.15098.710.0773.2246.3
5.647.110010.142.1796.8
4.935.6410010.1432.2456.9
4.484.9310010.1332.2667
4.164.4810010.1422.1647
3.914.1610010.1712.1647.1
3.723.9110010.1992.0787.1
3.553.7210010.2042.1067.1
3.423.5510010.2861.8757.1
3.33.4210010.3421.787.1
4.31509820.0251.5523.9
3.424.3178.720.0271.8424
2.993.4299.620.0411.9194.1
2.712.9999.820.0631.9494.1
2.522.7199.620.0971.9514.1
2.372.5299.720.1441.9514
2.252.3784.820.2062.0373.8
2.152.2574.720.2022.1683.1
2.072.1577.820.3112.0352.6
22.0763.820.3711.8422.2
ReflectionResolution: 1.85→50 Å / Num. all: 41159 / Num. obs: 41159 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Χ2: 1.902 / Net I/σ(I): 16.9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.65 / Num. unique all: 4037 / Rsym value: 0.425 / Χ2: 1.29 / % possible all: 97.7

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Phasing

PhasingMethod: SIRAS
Phasing set
ID
1
2
Phasing MIR der

Native set-ID: 1 / Reflection acentric: 3445 / Resolution: 4→35.93 Å

IDR cullis acentricR cullis centricDer set-IDReflection centric
ISO_1001818
ISO_20.8180.8742421
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricReflection acentricReflection centric
14.735.93ISO_1003832
10.8614.7ISO_1008844
910.86ISO_10012146
7.869ISO_10014654
7.067.86ISO_10017052
6.477.06ISO_10018460
66.47ISO_10020257
5.626ISO_10022147
5.315.62ISO_10024256
5.045.31ISO_10024855
4.815.04ISO_10026649
4.614.81ISO_10028360
4.434.61ISO_10028446
4.274.43ISO_10030259
4.134.27ISO_10031345
44.13ISO_10033756
14.735.93ISO_20.7060.7333816
10.8614.7ISO_20.7570.7988827
910.86ISO_20.771.05412122
7.869ISO_20.7840.74814629
7.067.86ISO_20.8230.95417024
6.477.06ISO_20.8230.87218430
66.47ISO_20.780.80820231
5.626ISO_20.8070.92922126
5.315.62ISO_20.8271.06124231
5.045.31ISO_20.8050.86124824
4.815.04ISO_20.8480.91326627
4.614.81ISO_20.8180.85128335
4.434.61ISO_20.821.11128419
4.274.43ISO_20.8470.75930233
4.134.27ISO_20.850.86431320
44.13ISO_20.8391.03233727

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
CNSrefinement
PDB_EXTRACT2data extraction
LOCALLYMODIFIED BLU-ICE GUI INTERFACE TO EPICS CONTROLdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.88→25.63 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1943 -RANDOM
Rwork0.235 ---
all0.243 39220 --
obs0.243 39220 97.7 %-
Displacement parametersBiso mean: 43.901 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2--2.75 Å20 Å2
3----4.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.88→25.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 31 450 3385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.88→2 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.329 341 -
Rwork0.313 --
obs-6199 99.3 %

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