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- PDB-4dyc: Crystal Structure of the terminase small subunit gp1 with D19R mu... -

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Basic information

Entry
Database: PDB / ID: 4dyc
TitleCrystal Structure of the terminase small subunit gp1 with D19R mutation of the bacterial virus sf6
ComponentsTerminase small subunit
KeywordsVIRAL PROTEIN / gp1 / DNA-binding
Function / homology: / Bacteriophage Sf6, terminase small subunit-like / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Terminase small subunit
Function and homology information
Biological speciesSalmonella phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terminase small subunit
B: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)31,1542
Polymers31,1542
Non-polymers00
Water3,693205
1
A: Terminase small subunit
B: Terminase small subunit

A: Terminase small subunit
B: Terminase small subunit

A: Terminase small subunit
B: Terminase small subunit

A: Terminase small subunit
B: Terminase small subunit


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 area32310 Å2
ΔGint-147 kcal/mol
Surface area44220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.570, 88.570, 73.550
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 Terminase small subunit


Mass: 15576.782 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage HK620 (virus) / Strain: bacteriophage Sf6 / Gene: gp1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLys / References: UniProt: Q9AZ01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.4
Details: 1.2M NAH2PO4/0.8M K2HPO4, 0.2M LI2SO4, pH 6.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2010
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 27710 / Num. obs: 27608 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.57 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.61
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 13.03 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 4.45 / Num. unique all: 1938 / % possible all: 97.1

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Processing

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

3hef


Resolution: 1.8→19.805 Å / SU ML: 0.02 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 4.45 / Phase error: 22.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1379 5 %Random
Rwork0.207 ---
obs0.2084 27574 99.64 %-
all-27710 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.089 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6427 Å20 Å20 Å2
2---3.6427 Å20 Å2
3---7.2854 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 0 205 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072011
X-RAY DIFFRACTIONf_angle_d0.9482710
X-RAY DIFFRACTIONf_dihedral_angle_d15.839763
X-RAY DIFFRACTIONf_chiral_restr0.068296
X-RAY DIFFRACTIONf_plane_restr0.004353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.86460.29911320.24532510X-RAY DIFFRACTION98
1.8646-1.93920.22221360.21042579X-RAY DIFFRACTION100
1.9392-2.02730.22891360.19662576X-RAY DIFFRACTION100
2.0273-2.13410.25221350.19532582X-RAY DIFFRACTION100
2.1341-2.26760.25271370.19822602X-RAY DIFFRACTION100
2.2676-2.44240.23691380.19482604X-RAY DIFFRACTION100
2.4424-2.68770.2531370.20752620X-RAY DIFFRACTION100
2.6877-3.07530.22411390.2072638X-RAY DIFFRACTION100
3.0753-3.86990.22431410.20012666X-RAY DIFFRACTION100
3.8699-19.8060.22811480.2112818X-RAY DIFFRACTION100

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