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- PDB-3zqo: Crystal structure of the small terminase oligomerization core dom... -

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Basic information

Entry
Database: PDB / ID: 3zqo
TitleCrystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 3)
ComponentsTERMINASE SMALL SUBUNIT
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / MOLECULAR MOTOR / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
J: TERMINASE SMALL SUBUNIT
K: TERMINASE SMALL SUBUNIT
L: TERMINASE SMALL SUBUNIT
M: TERMINASE SMALL SUBUNIT
N: TERMINASE SMALL SUBUNIT
O: TERMINASE SMALL SUBUNIT
P: TERMINASE SMALL SUBUNIT
Q: TERMINASE SMALL SUBUNIT
R: TERMINASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,28620
Polymers145,20818
Non-polymers782
Water10,881604
1
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)72,6049
Polymers72,6049
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19790 Å2
ΔGint-131.2 kcal/mol
Surface area24740 Å2
MethodPISA
2
J: TERMINASE SMALL SUBUNIT
K: TERMINASE SMALL SUBUNIT
L: TERMINASE SMALL SUBUNIT
M: TERMINASE SMALL SUBUNIT
N: TERMINASE SMALL SUBUNIT
O: TERMINASE SMALL SUBUNIT
P: TERMINASE SMALL SUBUNIT
Q: TERMINASE SMALL SUBUNIT
R: TERMINASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,68211
Polymers72,6049
Non-polymers782
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20440 Å2
ΔGint-135.5 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.202, 198.201, 59.202
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 8067.110 Da / Num. of mol.: 18 / Fragment: OLIGOMERIZATION CORE DOMAIN, RESIDUES 53-120
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): B834 / References: UniProt: Q1EJR8, UniProt: P68928*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.3 % / Description: NONE
Crystal growDetails: 2.7 M (NH4)2SO4, 0.2 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2008 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.534
11L, -K, H20.466
ReflectionResolution: 1.68→22.1 Å / Num. obs: 127549 / % possible obs: 85.6 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 98

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Processing

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

3zqm


Resolution: 1.68→22.1 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.191 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23357 1231 1 %RANDOM
Rwork0.18289 ---
obs0.18339 126317 83.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1--17.97 Å20 Å2-9.42 Å2
2--35.64 Å20 Å2
3----17.67 Å2
Refinement stepCycle: LAST / Resolution: 1.68→22.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7870 0 2 604 8476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227888
X-RAY DIFFRACTIONr_bond_other_d0.0020.025534
X-RAY DIFFRACTIONr_angle_refined_deg1.4172.00610507
X-RAY DIFFRACTIONr_angle_other_deg1.108313772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37651005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14726.436303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.473151771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4321536
X-RAY DIFFRACTIONr_chiral_restr0.0720.21275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028427
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021221
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_restr3.37337888
X-RAY DIFFRACTIONr_sphericity_free36.2345336
X-RAY DIFFRACTIONr_sphericity_bonded18.59758142
LS refinement shellResolution: 1.682→1.726 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 97 -
Rwork0.177 10454 -
obs--93.6 %

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