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- PDB-4zc3: DNA binding domain of small terminase SF6 phage -

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Basic information

Entry
Database: PDB / ID: 4zc3
TitleDNA binding domain of small terminase SF6 phage
ComponentsTerminase small subunit
KeywordsVIRAL PROTEIN / DNA binding domain
Function / homology
Function and homology information


chromosome organization / DNA binding / identical protein binding
Similarity search - Function
Terminase, small subunit, N-terminal DNA-binding domain, HTH motif / Terminase small subunit / : / Terminase small subunit / Terminase small subunit, N-terminal DNA-binding domain, HTH motif superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Terminase small subunit
Similarity search - Component
Biological speciesBacillus phage SF6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAntson, A.A. / Chechik, M. / Jenkins, H.T. / Greive, S.J.
Funding supportReunion, 1items
OrganizationGrant numberCountry
Wellcome TrustR1448101Reunion
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif.
Authors: Greive, S.J. / Fung, H.K. / Chechik, M. / Jenkins, H.T. / Weitzel, S.E. / Aguiar, P.M. / Brentnall, A.S. / Glousieau, M. / Gladyshev, G.V. / Potts, J.R. / Antson, A.A.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)7,6481
Polymers7,6481
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.545, 52.545, 54.877
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Terminase small subunit / G1P


Mass: 7647.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SF6 (virus) / Gene: small terminase / Plasmid: Champion pET SUMO / Details (production host): pYM295 / Production host: Escherichia coli (E. coli) / References: UniProt: P68928
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PACT premier screen (Molecular Dimensions) B2 0.1 M Malonate-Imidazole-Borate buffer 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→27.3 Å / Num. obs: 11127 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 33.67
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.42 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
ACORNphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→26.27 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.2453 / WRfactor Rwork: 0.2158 / FOM work R set: 0.8168 / SU B: 2.871 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0655 / SU Rfree: 0.0637 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 499 4.5 %RANDOM
Rwork0.1987 ---
obs0.1994 10628 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.5 Å2 / Biso mean: 32.969 Å2 / Biso min: 20.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.4→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms431 0 0 25 456
Biso mean---42.01 -
Num. residues----57
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019452
X-RAY DIFFRACTIONr_bond_other_d0.0020.02443
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.958610
X-RAY DIFFRACTIONr_angle_other_deg0.97231014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.03560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80723.63622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0581581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.846155
X-RAY DIFFRACTIONr_chiral_restr0.0870.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02106
X-RAY DIFFRACTIONr_mcbond_it1.4772.499231
X-RAY DIFFRACTIONr_mcbond_other1.4572.493230
X-RAY DIFFRACTIONr_mcangle_it2.2173.736288
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.52 47 -
Rwork0.449 777 -
all-824 -
obs--99.76 %
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)
12.84492.43010.4453.0676-0.50561.230.0614-0.0742-0.3018-0.2144-0.0618-0.22640.09670.0320.00040.1307-0.0139-0.04360.04050.01060.0485-6.582116.29357.3195
21.41421.61270.3823.4537-1.85023.3981-0.0562-0.00660.0967-0.10540.13390.235-0.0398-0.1671-0.07770.0851-0.0251-0.08420.05470.02190.0946-13.392623.25887.9981
30.547-0.49651.11312.14470.12663.03260.0368-0.0601-0.06040.06390.00360.18430.1245-0.1522-0.04030.0257-0.0250.01260.06850.02580.0512-11.742318.974415.8508
42.05820.8768-0.28780.5996-0.8353.3659-0.023-0.0839-0.1486-0.0961-0.0206-0.0519-0.02150.0250.04370.1141-0.0123-0.01810.06820.01060.01430.800823.37746.4202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 20
2X-RAY DIFFRACTION2A21 - 28
3X-RAY DIFFRACTION3A29 - 46
4X-RAY DIFFRACTION4A47 - 62

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