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- PDB-7cn6: T4 phage spackle protein gp61.3 -

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Basic information

Entry
Database: PDB / ID: 7cn6
TitleT4 phage spackle protein gp61.3
ComponentsProtein spackle
KeywordsVIRAL PROTEIN / Lysozyme inhibitor / Phage Lysis inhibition
Function / homologyProtein spackle / superinfection exclusion / host cell periplasmic space / Protein spackle
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKanamaru, S. / Leiman, P.G.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23121538 Japan
Japan Society for the Promotion of Science (JSPS)18H05421 Japan
CitationJournal: Viruses / Year: 2020
Title: Structure and Function of the T4 Spackle Protein Gp61.3.
Authors: Kanamaru, S. / Uchida, K. / Nemoto, M. / Fraser, A. / Arisaka, F. / Leiman, P.G.
History
DepositionJul 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein spackle
B: Protein spackle
C: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7496
Polymers26,6293
Non-polymers1203
Water7,188399
1
A: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9162
Polymers8,8761
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-8 kcal/mol
Surface area5150 Å2
MethodPISA
2
B: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9162
Polymers8,8761
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-9 kcal/mol
Surface area4990 Å2
MethodPISA
3
C: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9162
Polymers8,8761
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area5150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.376, 46.921, 75.277
Angle α, β, γ (deg.)90.000, 93.082, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Protein spackle


Mass: 8876.365 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: sp, 61.3 / Plasmid: pUC19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39230
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: PEG4000, glycine, calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→39.8 Å / Num. obs: 51366 / % possible obs: 95.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 11.76 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.107 / Rrim(I) all: 0.151 / Χ2: 0.83 / Net I/σ(I): 4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1001 / CC1/2: 0.895 / Rpim(I) all: 0.19 / Rrim(I) all: 0.269 / Χ2: 0.47 / % possible all: 75.4

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.9 Å / SU ML: 0.1797 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 28.4219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2279 2589 5.04 %
Rwork0.1789 48777 -
obs0.1814 51366 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.96 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 3 399 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211899
X-RAY DIFFRACTIONf_angle_d0.49342564
X-RAY DIFFRACTIONf_chiral_restr0.0348275
X-RAY DIFFRACTIONf_plane_restr0.0014343
X-RAY DIFFRACTIONf_dihedral_angle_d4.5167258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.28231110.20862051X-RAY DIFFRACTION72.82
1.63-1.670.25441180.2342194X-RAY DIFFRACTION75.75
1.67-1.70.2981990.21912312X-RAY DIFFRACTION79.36
1.7-1.740.23881540.21492424X-RAY DIFFRACTION85
1.74-1.780.32651400.2212600X-RAY DIFFRACTION89.69
1.78-1.830.26861430.22912757X-RAY DIFFRACTION96.73
1.83-1.890.27121820.21042823X-RAY DIFFRACTION98.23
1.89-1.950.25841480.20052819X-RAY DIFFRACTION99.36
1.95-2.020.24531210.19222974X-RAY DIFFRACTION99.68
2.02-2.10.2121390.18292835X-RAY DIFFRACTION99.7
2.1-2.190.24331480.17732892X-RAY DIFFRACTION99.87
2.19-2.310.23451580.18292833X-RAY DIFFRACTION99.73
2.31-2.450.21031620.17162885X-RAY DIFFRACTION99.9
2.45-2.640.28971390.18422891X-RAY DIFFRACTION100
2.64-2.910.22941210.18812909X-RAY DIFFRACTION99.9
2.91-3.330.21331600.16612899X-RAY DIFFRACTION99.87
3.33-4.180.18381820.14032819X-RAY DIFFRACTION99.54
4.18-19.90.19791640.15872860X-RAY DIFFRACTION99.54

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