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

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Basic information

Entry
Database: PDB / ID: 2wbn
TitleCrystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1
ComponentsTERMINASE LARGE SUBUNIT
KeywordsVIRAL PROTEIN / LARGE TERMINASE / NUCLEASE / DNA PACKAGING
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 / SYNCHROTRON / MAD / Resolution: 1.9 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 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Database references / Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TERMINASE LARGE SUBUNIT


Theoretical massNumber of molelcules
Total (without water)24,2971
Polymers24,2971
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.915, 69.915, 72.681
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 16389 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.3 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→60.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.806 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 834 5.1 %RANDOM
Rwork0.195 ---
obs0.197 15671 98.9 %-
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: 40.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 0 127 1586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221489
X-RAY DIFFRACTIONr_bond_other_d0.0010.021053
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9562012
X-RAY DIFFRACTIONr_angle_other_deg0.83132542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36323.88285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54315264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1741516
X-RAY DIFFRACTIONr_chiral_restr0.0730.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
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_it0.6121.5889
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08421440
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7513600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7864.5572
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 60 -
Rwork0.262 1033 -
obs--90.78 %
Refinement TLS params.Method: refined / Origin x: 15.293 Å / Origin y: 26.742 Å / Origin z: 21.877 Å
111213212223313233
T-0.0113 Å20.1482 Å20.0068 Å2--0.0791 Å2-0.0021 Å2---0.1493 Å2
L2.237 °2-0.9295 °20.314 °2-3.749 °2-0.3744 °2--1.5432 °2
S0.2125 Å °0.3325 Å °0.0167 Å °-0.6332 Å °-0.214 Å °-0.0647 Å °0.189 Å °-0.0205 Å °0.0015 Å °

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