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- PDB-4idh: Crystal Structure of the large terminase subunit gp2 of bacterial... -

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Basic information

Entry
Database: PDB / ID: 4idh
TitleCrystal Structure of the large terminase subunit gp2 of bacterial virus Sf6
ComponentsGene 2 protein
KeywordsVIRAL PROTEIN / DNA packaging / terminase / ATPase / nuclease / ATP binding / Magnesium binding
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Terminase RNAseH like domain / Phage terminase large subunit, N-terminal / Phage terminase large subunit / Bacteriophage terminase, large subunit / Nucleotidyltransferase; domain 5 - #240 / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Terminase RNAseH like domain / Phage terminase large subunit, N-terminal / Phage terminase large subunit / Bacteriophage terminase, large subunit / Nucleotidyltransferase; domain 5 - #240 / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesShigella phage Sf6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsZhao, H. / Christensen, T. / Kamau, Y. / Tang, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage.
Authors: Zhao, H. / Christensen, T.E. / Kamau, Y.N. / Tang, L.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gene 2 protein


Theoretical massNumber of molelcules
Total (without water)55,2481
Polymers55,2481
Non-polymers00
Water10,611589
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.790, 63.440, 150.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Gene 2 protein /


Mass: 55247.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf6 (virus) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q716H3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris, 15% ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03304 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 21, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03304 Å / Relative weight: 1
ReflectionResolution: 1.69→42.72 Å / Num. all: 62855 / Num. obs: 62415 / % possible obs: 99.3 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 7.1
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.3 / Num. unique all: 9076 / % possible all: 100

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: nuclease domain of gp2 of bacterial virus sf6 and ATPase domain of gp17 of T4 bacteriophage

Resolution: 1.69→19.859 Å / SU ML: 0.19 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 3117 5 %Random
Rwork0.1811 ---
obs0.1828 62324 98.95 %-
all-62855 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.51 Å2
Refinement stepCycle: LAST / Resolution: 1.69→19.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 0 589 4185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073731
X-RAY DIFFRACTIONf_angle_d1.025058
X-RAY DIFFRACTIONf_dihedral_angle_d12.3751419
X-RAY DIFFRACTIONf_chiral_restr0.074545
X-RAY DIFFRACTIONf_plane_restr0.004660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.71540.34511430.26532709X-RAY DIFFRACTION100
1.7154-1.74350.27421390.2472651X-RAY DIFFRACTION100
1.7435-1.77350.2691400.24732671X-RAY DIFFRACTION100
1.7735-1.80580.30631440.23342709X-RAY DIFFRACTION100
1.8058-1.84050.27641390.22572657X-RAY DIFFRACTION100
1.8405-1.8780.23321420.21442700X-RAY DIFFRACTION100
1.878-1.91880.38931420.32152691X-RAY DIFFRACTION100
1.9188-1.96340.31961400.26922665X-RAY DIFFRACTION100
1.9634-2.01250.20731430.18242693X-RAY DIFFRACTION100
2.0125-2.06680.211420.16792712X-RAY DIFFRACTION100
2.0668-2.12760.23611410.16852684X-RAY DIFFRACTION100
2.1276-2.19620.17161420.16932710X-RAY DIFFRACTION100
2.1962-2.27450.32841430.26032694X-RAY DIFFRACTION99
2.2745-2.36550.22381400.17332676X-RAY DIFFRACTION99
2.3655-2.47290.19011420.16772689X-RAY DIFFRACTION99
2.4729-2.60310.17571430.16322708X-RAY DIFFRACTION99
2.6031-2.76570.23141410.16682687X-RAY DIFFRACTION99
2.7657-2.97860.19921410.172679X-RAY DIFFRACTION98
2.9786-3.27720.18971410.17382680X-RAY DIFFRACTION97
3.2772-3.74860.18681420.15512694X-RAY DIFFRACTION97
3.7486-4.71240.15971430.14322714X-RAY DIFFRACTION97
4.7124-19.86020.21281440.17412734X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98930.24430.24451.32950.13441.97620.0805-0.0436-0.12970.23620.0147-0.2070.13050.1648-0.0790.19790.0303-0.04840.13390.00580.167429.506343.494125.6209
23.179-0.25081.75162.3229-0.13683.4294-0.1858-0.1895-0.39410.00110.30560.35380.0952-0.2861-0.10650.32710.0370.00230.2380.06690.238618.964535.420145.9259
31.2327-0.1696-0.14771.7367-0.02831.03630.02620.0146-0.0158-0.0251-0.0043-0.02830.029-0.0025-0.01270.0687-0.0033-0.01910.1028-0.01690.091846.732939.156567.2087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:173)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 174:211)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 212:465)A0

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