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- PDB-4dzp: Crystal structure of the terminase small subunit gp1 with R48A mu... -

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Basic information

Entry
Database: PDB / ID: 4dzp
TitleCrystal structure of the terminase small subunit gp1 with R48A mutation of the bacterial virus sf6
ComponentsGene 1 protein
KeywordsVIRAL PROTEIN / gp1 / DNA-binding / R48A 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: 1.8 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
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)30,9812
Polymers30,9812
Non-polymers00
Water3,837213
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)123,9258
Polymers123,9258
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 area32280 Å2
ΔGint-144 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.060, 89.060, 72.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-293-

HOH

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Components

#1: Protein Gene 1 protein


Mass: 15490.663 Da / Num. of mol.: 2 / Mutation: R48A
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.: 213 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
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: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2010 / Details: Rh coated
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→19.221 Å / Num. all: 27730 / Num. obs: 27623 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.38 % / Biso Wilson estimate: 26.637 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 31.71
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 8.78 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 7.78 / Num. unique all: 1977 / % possible all: 98.9

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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: PDB code 3HEF

3hef


Resolution: 1.8→19.221 Å / SU ML: 0.01 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1380 5 %RANDOM
Rwork0.209 ---
obs0.2111 27592 99.63 %-
all-27730 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.394 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 35.88 Å2
Baniso -1Baniso -2Baniso -3
1--4.4261 Å2-0 Å20 Å2
2---4.4261 Å20 Å2
3---8.8522 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 0 213 2180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062005
X-RAY DIFFRACTIONf_angle_d0.8592704
X-RAY DIFFRACTIONf_dihedral_angle_d15.215757
X-RAY DIFFRACTIONf_chiral_restr0.064296
X-RAY DIFFRACTIONf_plane_restr0.004353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.86450.24651350.22092551X-RAY DIFFRACTION99
1.8645-1.93910.21241360.20042586X-RAY DIFFRACTION100
1.9391-2.02720.27591360.20292584X-RAY DIFFRACTION100
2.0272-2.1340.21661360.20272587X-RAY DIFFRACTION100
2.134-2.26750.25481360.19872589X-RAY DIFFRACTION100
2.2675-2.44230.21881380.19532609X-RAY DIFFRACTION100
2.4423-2.68740.20951370.20892612X-RAY DIFFRACTION100
2.6874-3.0750.23921390.21292631X-RAY DIFFRACTION99
3.075-3.86890.23531400.20722671X-RAY DIFFRACTION99
3.8689-19.2220.29321470.21282792X-RAY DIFFRACTION99

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