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- PDB-3zqp: Crystal structure of the small terminase oligomerization domain f... -

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Basic information

Entry
Database: PDB / ID: 3zqp
TitleCrystal structure of the small terminase oligomerization domain 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
Helix Hairpins - #2160 / Terminase small subunit / : / Terminase small subunit / Terminase small subunit, N-terminal DNA-binding domain, HTH motif superfamily / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Terminase small subunit / Terminase small subunit
Similarity search - Component
Biological speciesBACILLUS PHAGE SF6 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)162,6269
Polymers162,6269
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36270 Å2
ΔGint-196.1 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.271, 74.271, 119.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 18069.576 Da / Num. of mol.: 9
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: 2.38 Å3/Da / Density % sol: 48.4 %
Description: MR WAS PERFORMED USING THREE NEIGHBORING SUBUNITS
Crystal growDetails: 0.2 M MGCL2, 8% PEG 550MME, 0.1 M TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDate: Feb 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→43.8 Å / Num. obs: 14792 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 3→3.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZQM

3zqm


Resolution: 3→25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.564 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22592 746 5 %RANDOM
Rwork0.18516 ---
obs0.18714 14036 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.815 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0.68 Å20 Å2
2---1.36 Å20 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5289 0 0 0 5289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225316
X-RAY DIFFRACTIONr_bond_other_d0.0040.023584
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9737123
X-RAY DIFFRACTIONr_angle_other_deg0.85138933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2165674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02926.8225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.282151127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2121518
X-RAY DIFFRACTIONr_chiral_restr0.0650.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025717
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02845
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 56 -
Rwork0.327 1058 -
obs--100 %

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