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- PDB-3hef: Crystal structure of the bacteriophage Sf6 terminase small subunit -

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Basic information

Entry
Database: PDB / ID: 3hef
TitleCrystal structure of the bacteriophage Sf6 terminase small subunit
ComponentsGene 1 protein
KeywordsVIRAL PROTEIN / bacteriophage Sf6 / terminase small subunit gp1 / gp1 octameric assembly / gp1 channel / DNA recognition / DNA packaging
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 speciesEnterobacteria phage Sf6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsZhao, H. / Tang, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine
Authors: Zhao, H. / Finch, C.J. / Sequeira, R.D. / Johnson, B.A. / Johnson, J.E. / Casjens, S.R. / Tang, L.
History
DepositionMay 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,7182
Polymers31,7182
Non-polymers00
Water4,576254
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)126,8728
Polymers126,8728
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 area32030 Å2
ΔGint-155 kcal/mol
Surface area44010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.858, 88.858, 72.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Gene 1 protein


Mass: 15859.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Sf6 (virus) / Gene: gp1 / Plasmid: pET28b / 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.: 254 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2M NaH2PO4/0.8M K2HPO4, 0.2M Li2SO4, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.02462
SYNCHROTRONSSRL BL7-120.9791
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 26, 2009flat mirrors
MARMOSAIC 325 mm CCD2CCDFeb 26, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Side scattering bent cube-root I-beam single crystalSINGLE WAVELENGTHMx-ray1
2side scattering I-beam bent single crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.024621
20.97911
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 107.12 / Number: 176519 / Rmerge(I) obs: 0.065 / Χ2: 1.8 / D res high: 1.86 Å / D res low: 50 Å / Num. obs: 24582 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.015094.310.044.926.8
3.184.019810.0462.8277
2.783.1898.610.0612.0657.2
2.522.789910.0691.3657.2
2.342.5299.310.0811.1677.2
2.212.3499.410.1221.317.3
2.092.2199.510.1581.0657.3
22.0999.610.2391.1887.3
1.93299.810.361.047.2
1.861.9399.910.5061.1577.3
ReflectionResolution: 1.65→50 Å / Num. all: 35754 / Num. obs: 35647 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 28.4 % / Rmerge(I) obs: 0.053 / Χ2: 1.925 / Net I/σ(I): 107.121
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 28.6 % / Rmerge(I) obs: 0.521 / Num. unique all: 3521 / Χ2: 1.223 / % possible all: 100

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Phasing

Phasing dmFOM : 0.57 / FOM acentric: 0.56 / FOM centric: 0.61 / Reflection: 24251 / Reflection acentric: 21281 / Reflection centric: 2970
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.3-39.7050.930.950.91075756319
3.3-5.30.930.930.8932952716579
2.7-3.30.80.810.7541273580547
2.3-2.70.620.630.5641093650459
2-2.30.410.420.3872486548700
1.9-20.190.190.1743974031366

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.851 / σ(F): 1037 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1665 4.7 %RANDOM
Rwork0.224 ---
all-35552 --
obs-33097 93.1 %-
Solvent computationBsol: 63.494 Å2
Displacement parametersBiso max: 95.21 Å2 / Biso mean: 35.237 Å2 / Biso min: 11.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.895 Å20 Å20 Å2
2---3.895 Å20 Å2
3---7.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 254 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2321.5
X-RAY DIFFRACTIONc_scbond_it2.2192
X-RAY DIFFRACTIONc_mcangle_it1.9072
X-RAY DIFFRACTIONc_scangle_it3.3092.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.311 257 -
Rwork0.265 --
obs-4989 90.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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