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- PDB-3zqq: Crystal structure of the full-length small terminase from a SPP1-... -

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Basic information

Entry
Database: PDB / ID: 3zqq
TitleCrystal structure of the full-length small terminase from a SPP1-like bacteriophage
ComponentsTERMINASE SMALL SUBUNIT
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DNA PACKAGING
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 / Helix Hairpins - #2160 / Terminase small subunit / Terminase small subunit, N-terminal DNA-binding domain, HTH motif superfamily / Terminase small subunit / Helix Hairpins / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Terminase small subunit / Terminase small subunit
Similarity search - Component
Biological speciesBACILLUS PHAGE SF6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsButtner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Alonso, J.C. / Antson, A.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Basis for DNA Recognition and Loading Into a Viral Packaging Motor.
Authors: Buttner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Ebong, I.O. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Robinson, C.V. / Alonso, J.C. / Antson, A.A.
History
DepositionJun 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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


Theoretical massNumber of molelcules
Total (without water)54,2093
Polymers54,2093
Non-polymers00
Water0
1
A: TERMINASE SMALL SUBUNIT
B: TERMINASE SMALL SUBUNIT
C: TERMINASE SMALL SUBUNIT

A: TERMINASE SMALL SUBUNIT
B: TERMINASE SMALL SUBUNIT
C: TERMINASE SMALL SUBUNIT

A: TERMINASE SMALL SUBUNIT
B: TERMINASE SMALL SUBUNIT
C: TERMINASE SMALL SUBUNIT


Theoretical massNumber of molelcules
Total (without water)162,6269
Polymers162,6269
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area40320 Å2
ΔGint-219.3 kcal/mol
Surface area47990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.184, 98.184, 323.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein TERMINASE SMALL SUBUNIT / SF6 SMALL TERMINASE G1P


Mass: 18069.576 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE SF6 (virus) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1EJR8, UniProt: P68928*PLUS

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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: 3.07 Å3/Da / Density % sol: 60 %
Description: MR WAS PERFORMED USING THREE NEIGHBORING SUBUNITS
Crystal growDetails: 0.2 M MGCL2, 8 % PEG 2000, 8 % PEG 550MME, 0.1 M TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 4.01→107 Å / Num. obs: 3308 / % possible obs: 62 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.6
Reflection shellResolution: 4.01→4.23 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.1 / % possible all: 18

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Processing

Software
NameVersionClassification
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2CMP AND 3ZQP

2cmp

3zqp


Resolution: 4→107 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE THIRD DNA-BINDING DOMAIN (DBD OF CHAIN B) IS NOT SUFFICIENTLY DEFINED IN THE ELECTRON DENSITY AND WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 482 9 %RANDOM
Rwork0.1996 ---
obs0.1996 3308 61.5 %-
Solvent computationBsol: 207.145 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 220 Å2
Baniso -1Baniso -2Baniso -3
1--86.76 Å20 Å20 Å2
2---86.76 Å20 Å2
3---173.52 Å2
Refinement stepCycle: LAST / Resolution: 4→107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 0 0 2646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00201
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.65967
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.01→4.23 Å / Rfactor Rfree: 0.2011 / Rfactor Rwork: 0.2026 / Total num. of bins used: 10
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM

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