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- PDB-5m1q: Crystal structure of the large terminase nuclease from thermophil... -

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Basic information

Entry
Database: PDB / ID: 5m1q
TitleCrystal structure of the large terminase nuclease from thermophilic phage G20c with bound Zinc
ComponentsPhage terminase large subunit
KeywordsVIRAL PROTEIN / large terminase / nuclease domain
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 speciesThermus phage G20c (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsXu, R.G. / Jenkins, H.T. / Chechik, M. / Blagova, E.V. / Greive, S.J. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism.
Authors: Xu, R.G. / Jenkins, H.T. / Chechik, M. / Blagova, E.V. / Lopatina, A. / Klimuk, E. / Minakhin, L. / Severinov, K. / Greive, S.J. / Antson, A.A.
History
DepositionOct 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3May 1, 2024Group: 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage terminase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0805
Polymers20,8181
Non-polymers2624
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-114 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.983, 60.983, 90.396
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Phage terminase large subunit


Mass: 20818.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: scientific_name: 'Thermus phage G20c' ncbi_taxonomy_id: 1406341 The same as entry.id 4XVN
Source: (gene. exp.) Thermus phage G20c (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4BKS3*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.01 M Zinc chloride, 0.1 M MES pH 6.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→45.6 Å / Num. obs: 33635 / % possible obs: 99.7 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.045 / Rrim(I) all: 0.097 / Net I/σ(I): 8.2 / Num. measured all: 151672
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.45-1.473.91.2910.42199.5
7.94-45.64.40.0470.997198.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 1.45→45.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.601 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1603 4.8 %RANDOM
Rwork0.2014 ---
obs0.2019 32017 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.46 Å2 / Biso mean: 23.601 Å2 / Biso min: 10.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: final / Resolution: 1.45→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 5 107 1418
Biso mean--24.27 33.37 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191373
X-RAY DIFFRACTIONr_bond_other_d0.0020.021285
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9741872
X-RAY DIFFRACTIONr_angle_other_deg0.83632949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61224.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57315222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.97157
X-RAY DIFFRACTIONr_chiral_restr0.0650.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02303
X-RAY DIFFRACTIONr_mcbond_it1.4472.274706
X-RAY DIFFRACTIONr_mcbond_other1.4462.272705
X-RAY DIFFRACTIONr_mcangle_it2.3763.389886
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 141 -
Rwork0.324 2343 -
all-2484 -
obs--99.56 %

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