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- PDB-4dyq: High resolution crystal structure of terminase small subunit gp1 ... -

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Basic information

Entry
Database: PDB / ID: 4dyq
TitleHigh resolution crystal structure of terminase small subunit gp1 of the bacterial virus sf6
ComponentsGene 1 protein
KeywordsVIRAL PROTEIN / gp1 / octamer / DNA-binding
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: 1.502 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 29, 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
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: Gene 1 protein
B: Gene 1 protein


Theoretical massNumber of molelcules
Total (without water)31,1542
Polymers31,1542
Non-polymers00
Water4,756264
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 area32170 Å2
ΔGint-144 kcal/mol
Surface area43840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.705, 88.705, 72.394
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: 15576.782 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
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: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2009 / Details: Rh coated flat mirror
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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 46607 / Num. obs: 45628 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 19.318 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 50.183
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4462 / Rsym value: 0.503 / % possible all: 97.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HEF

3hef


Resolution: 1.502→19.125 Å / SU ML: 0.14 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1925 4.38 %Random
Rwork0.1769 ---
obs0.178 43953 94.41 %-
all-46607 --
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.241 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 19.318 Å2
Baniso -1Baniso -2Baniso -3
1--2.938 Å2-0 Å20 Å2
2---2.938 Å20 Å2
3---5.876 Å2
Refinement stepCycle: LAST / Resolution: 1.502→19.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 264 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052029
X-RAY DIFFRACTIONf_angle_d0.8912735
X-RAY DIFFRACTIONf_dihedral_angle_d12.692780
X-RAY DIFFRACTIONf_chiral_restr0.051297
X-RAY DIFFRACTIONf_plane_restr0.005358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5023-1.53980.25231170.24652626X-RAY DIFFRACTION84
1.5398-1.58140.25091320.24242809X-RAY DIFFRACTION90
1.5814-1.62790.23231300.21932876X-RAY DIFFRACTION92
1.6279-1.68050.22041360.20032970X-RAY DIFFRACTION94
1.6805-1.74050.19951370.192973X-RAY DIFFRACTION95
1.7405-1.81010.2161360.18412999X-RAY DIFFRACTION95
1.8101-1.89240.22241400.17593029X-RAY DIFFRACTION97
1.8924-1.99210.19481380.17463063X-RAY DIFFRACTION97
1.9921-2.11680.18071440.16613095X-RAY DIFFRACTION98
2.1168-2.280.18851430.16053124X-RAY DIFFRACTION98
2.28-2.50890.16481420.15163108X-RAY DIFFRACTION98
2.5089-2.87090.19481430.17423125X-RAY DIFFRACTION97
2.8709-3.61310.20511450.16623135X-RAY DIFFRACTION96
3.6131-19.12660.21411420.18673096X-RAY DIFFRACTION90
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)
13.3060.66-1.25470.3301-0.4762.70790.56480.25111.3813-0.01550.15970.1558-0.28590.2558-0.59480.2970.11870.03490.24430.05730.72736.335435.355116.89
20.7171-0.0868-0.04350.94720.50720.87170.0445-0.05860.10850.02590.0098-0.0618-0.0452-0.0289-0.04530.1616-0.00930.00660.1644-0.00740.183749.024911.889817.7052
31.8285-0.1891-0.24160.69230.09510.95410.0633-0.0270.56350.16740.0158-0.2943-0.0397-0.0308-0.05650.3036-0.06540.01420.243-0.00190.395764.046230.444719.3956
40.52420.0964-0.03651.08390.38020.4824-0.0148-0.00860.0473-0.07610.0486-0.0773-0.12620.0343-0.02330.16320.0041-0.00710.1562-0.00660.18353.4955.033515.1209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 10:63
2X-RAY DIFFRACTION2chain A and resseq 64:132
3X-RAY DIFFRACTION3chain B and resseq 10:63
4X-RAY DIFFRACTION4chain B and resseq 64:139

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