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- PDB-2wc9: Crystal structure of the g2p (large terminase) nuclease domain fr... -

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Basic information

Entry
Database: PDB / ID: 2wc9
TitleCrystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1 with bound Mn
ComponentsTERMINASE LARGE SUBUNIT
KeywordsVIRAL PROTEIN / DNA TRANSLOCATION
Function / homology
Function and homology information


viral terminase, large subunit / viral DNA genome packaging / nuclease activity / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Phage terminase large subunit, C-terminal / Terminase, large subunit SPP1-like / Nucleotidyltransferase; domain 5 - #280 / Terminase RNAseH like domain / Phage terminase large subunit, N-terminal / Phage terminase large subunit / Bacteriophage terminase, large subunit / 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 speciesBACILLUS PHAGE SPP1 (virus)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsSmits, C. / Chechik, M. / Kovalevskiy, O.V. / Shevtsov, M.B. / Foster, A.W. / Alonso, J.C. / Antson, A.A.
CitationJournal: Embo Rep. / Year: 2009
Title: Structural Basis for the Nuclease Activity of a Bacteriophage Large Terminase.
Authors: Smits, C. / Chechik, M. / Kovalevskiy, O.V. / Shevtsov, M.B. / Foster, A.W. / Alonso, J.C. / Antson, A.A.
History
DepositionMar 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TERMINASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5034
Polymers24,2971
Non-polymers2063
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.710, 69.710, 73.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TERMINASE LARGE SUBUNIT / G2P


Mass: 24296.648 Da / Num. of mol.: 1 / Fragment: NUCLEASE DOMAIN, RESIDUES 232-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE SPP1 (virus) / Plasmid: PYM20 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P54308
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 80 MM TRIS PH 8.5, 2.3 M LI2SO4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Sep 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→60.4 Å / Num. obs: 7520 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→24.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.218 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25862 349 4.7 %RANDOM
Rwork0.19502 ---
obs0.19781 7142 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.121 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å20 Å2
2---0.21 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 7 24 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221484
X-RAY DIFFRACTIONr_bond_other_d0.0010.021043
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9582007
X-RAY DIFFRACTIONr_angle_other_deg0.81432517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68623.88285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21615260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6051516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3161.5884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.62421432
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0753600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7684.5575
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 21 -
Rwork0.278 512 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.293 Å / Origin y: 26.742 Å / Origin z: 21.877 Å
111213212223313233
T0.2141 Å20.1099 Å2-0.07 Å2-0.1527 Å2-0.0756 Å2--0.0759 Å2
L2.3011 °2-1.1015 °20.8874 °2-7.5522 °20.5877 °2--3.8026 °2
S0.014 Å °0.1473 Å °-0.082 Å °-0.7741 Å °0.0772 Å °-0.1136 Å °-0.0349 Å °0.1882 Å °-0.0912 Å °

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