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- PDB-6ejq: Crystal structure of a C-terminally truncated small terminase pro... -

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Basic information

Entry
Database: PDB / ID: 6ejq
TitleCrystal structure of a C-terminally truncated small terminase protein from the thermophilic bacteriophage G20c
ComponentsTerminase small subunit
KeywordsVIRAL PROTEIN / Small terminase
Function / homology: / : / Phage G20C small terminase, N-terminal domain / Phage G20C small terminase C-terminal domain / DNA binding / Terminase, small subunit
Function and homology information
Biological speciesThermus phage G20c (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, R.G. / Loredo-Varela, J. / Jenkins, H.T. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a C-terminally truncated small terminase protein from the thermophilic bacteriophage G20c
Authors: Xu, R.G. / Loredo-Varela, J. / Jenkins, H.T. / Antson, A.A.
History
DepositionSep 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminase small subunit
B: Terminase small subunit
C: Terminase small subunit
D: Terminase small subunit
E: Terminase small subunit
F: Terminase small subunit
G: Terminase small subunit
H: Terminase small subunit
I: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)142,2489
Polymers142,2489
Non-polymers00
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, nonamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30630 Å2
ΔGint-238 kcal/mol
Surface area56210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.275, 167.275, 139.732
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
Terminase small subunit


Mass: 15805.306 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: Two helices of chain E haven't been model due to poor density.
Source: (gene. exp.) Thermus phage G20c (virus) / Gene: G20c_79 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4BKP6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 3.6 Å3/Da / Density % sol: 65.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 35% v/v Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→49.47 Å / Num. obs: 88169 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.035 / Rrim(I) all: 0.131 / Net I/σ(I): 16.1 / Num. measured all: 1187820 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3413.51.8115992544510.5990.5111.8831.6100
12.39-49.4710.10.02967696700.9990.010.03165.498.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVN

4xvn


Resolution: 2.3→49.47 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.596 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 4404 5 %RANDOM
Rwork0.2079 ---
obs0.2094 83699 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.1 Å2 / Biso mean: 56.049 Å2 / Biso min: 23.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 2.3→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8909 0 0 656 9565
Biso mean---52.29 -
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199127
X-RAY DIFFRACTIONr_bond_other_d0.0010.028937
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.99812354
X-RAY DIFFRACTIONr_angle_other_deg0.874320615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9951160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52324.106414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.956151693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4561589
X-RAY DIFFRACTIONr_chiral_restr0.0570.21471
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021729
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 344 -
Rwork0.288 6077 -
all-6421 -
obs--99.95 %

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