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- PDB-4dzj: Crystal structure of the terminase small subunit gp1 with K59E mu... -

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Basic information

Entry
Database: PDB / ID: 4dzj
TitleCrystal structure of the terminase small subunit gp1 with K59E mutation of the bacterial virus sf6
ComponentsGene 1 protein
KeywordsVIRAL PROTEIN / gp1 / octamer / DNA-binding / K59E mutation
Function / homology: / Bacteriophage Sf6, terminase small subunit-like / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / identical protein binding / Gene 1 protein
Function and homology information
Biological speciesShigella phage Sf6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhao, H. / Tang, L.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural and Functional Studies of the Phage Sf6 Terminase Small Subunit Reveal a DNA-Spooling Device Facilitated by Structural Plasticity.
Authors: Zhao, H. / Kamau, Y.N. / Christensen, T.E. / Tang, L.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gene 1 protein
B: Gene 1 protein


Theoretical massNumber of molelcules
Total (without water)31,1532
Polymers31,1532
Non-polymers00
Water4,918273
1
A: Gene 1 protein
B: Gene 1 protein

A: Gene 1 protein
B: Gene 1 protein

A: Gene 1 protein
B: Gene 1 protein

A: Gene 1 protein
B: Gene 1 protein


Theoretical massNumber of molelcules
Total (without water)124,6148
Polymers124,6148
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area32380 Å2
ΔGint-142 kcal/mol
Surface area44040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.740, 88.740, 72.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Gene 1 protein


Mass: 15576.716 Da / Num. of mol.: 2 / Mutation: K59E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella phage Sf6 (virus) / Strain: bacteriophage Sf6 / Gene: gp1 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: Q716H4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.2M NAH2PO4/0.8M K2HPO4, 0.2M Li2SO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2009
Details: flat collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 23620 / Num. obs: 23597 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 25.356 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 60.556
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 6.733 / Num. unique all: 2307 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HEF

3hef


Resolution: 1.9→19.843 Å / SU ML: 1.64 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1141 4.98 %RANDOM
Rwork0.1991 ---
obs0.2009 22912 97.18 %-
all-23597 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.095 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8857 Å2-0 Å20 Å2
2---3.8857 Å20 Å2
3---7.7713 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 273 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062017
X-RAY DIFFRACTIONf_angle_d0.8452720
X-RAY DIFFRACTIONf_dihedral_angle_d15.829765
X-RAY DIFFRACTIONf_chiral_restr0.061296
X-RAY DIFFRACTIONf_plane_restr0.004357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8993-1.98560.27241300.2032495X-RAY DIFFRACTION90
1.9856-2.09020.23691360.19382623X-RAY DIFFRACTION96
2.0902-2.2210.26171400.19492676X-RAY DIFFRACTION98
2.221-2.39220.23041400.1892693X-RAY DIFFRACTION98
2.3922-2.63250.24631450.19242716X-RAY DIFFRACTION98
2.6325-3.01220.23091450.20092769X-RAY DIFFRACTION99
3.0122-3.79080.22161480.18882819X-RAY DIFFRACTION100
3.7908-19.84390.23011570.20722980X-RAY DIFFRACTION100

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