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- PDB-2cmp: crystal structure of the DNA binding domain of G1P SMALL TERMINAS... -

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Basic information

Entry
Database: PDB / ID: 2cmp
Titlecrystal structure of the DNA binding domain of G1P SMALL TERMINASE SUBUNIT from bacteriophage SF6
ComponentsTERMINASE SMALL SUBUNIT
KeywordsVIRAL PROTEIN / SF6 / 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 / 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 speciesBACTERIOPHAGE SF6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsBenini, S. / Chechik, M. / Ortiz-Lombardia, M. / Polier, S. / Shevtsov, M.B. / DeLuchi, D. / Alonso, J.C. / Antson, A.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The 1.58 A Resolution Structure of the DNA-Binding Domain of Bacteriophage Sf6 Small Terminase Provides New Hints on DNA Binding
Authors: Benini, S. / Chechik, M. / Ortiz-Lombardia, M. / Polier, S. / Leech, A. / Shevtsov, M.B. / Alonso, J.C.
History
DepositionMay 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 10, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Revision 1.3Apr 17, 2013Group: Database references / Source and taxonomy
Revision 1.4May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_validate_polymer_linkage
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TERMINASE SMALL SUBUNIT


Theoretical massNumber of molelcules
Total (without water)6,9601
Polymers6,9601
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.286, 57.286, 57.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2021-

HOH

21A-2033-

HOH

31A-2034-

HOH

41A-2051-

HOH

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Components

#1: Protein TERMINASE SMALL SUBUNIT / G1P


Mass: 6959.960 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN, RESIDUES 1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE SF6 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P68928
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Compound detailsESSENTIAL FOR DNA MATURATION AND PACKAGING.
Sequence detailsTHE FIRST THREE RESIDUES (GSH) IN THE SEQUENCE ARE THE REMNANT OF THE HISTIDINE TAG AFTER THROMBIN CLEAVAGE.

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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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP WITH 1 UL OF 17MG/ML PROTEIN IN 50MM HEPES PH7.5 10MM NACL MIXED WITH 1 UL OF 2.4 M NA MALONATE PH 7.0 AND EQUILIBRATED AGAINST 1ML OF 2.4 M NA MALONATE PH 7.0 AT 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9765
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.58→23.4 Å / Num. obs: 8787 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 38.7
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→40.52 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.699 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROTEIN MODEL STARTS FROM RESIDUE LYS5
RfactorNum. reflection% reflectionSelection details
Rfree0.276 408 4.7 %RANDOM
Rwork0.225 ---
obs0.227 8363 99.9 %-
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: 46.07 Å2
Refinement stepCycle: LAST / Resolution: 1.58→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms435 0 0 52 487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022489
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.989655
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.226562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43923.33321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7521598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.898155
X-RAY DIFFRACTIONr_chiral_restr0.0930.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02363
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.2261
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2335
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5512315
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5043492
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7926189
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7818162
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: 1.58→1.63 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 34
Rwork0.255 614
Refinement TLS params.Method: refined / Origin x: 22.3653 Å / Origin y: 8.6614 Å / Origin z: 34.0326 Å
111213212223313233
T-0.097 Å20.043 Å20.0411 Å2--0.1728 Å20.0324 Å2---0.2046 Å2
L4.9987 °2-2.0793 °2-1.1712 °2-8.4345 °2-1.0353 °2--3.6795 °2
S0.1184 Å °0.2874 Å °0.3552 Å °0.5306 Å °-0.2609 Å °-0.2456 Å °-0.3382 Å °-0.3009 Å °0.1425 Å °

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