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- PDB-6hp7: ARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE in complex with 43 m... -

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Basic information

Entry
Database: PDB / ID: 6hp7
TitleARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE in complex with 43 mer DNA
Components
  • (DNA (43-MER)) x 2
  • SPBc2 prophage-derived uncharacterized protein YopK
KeywordsDNA BINDING PROTEIN / Arbitrium peptide receptor / SPbeta phage
Function / homology: / PHOSPHATE ION / DNA / DNA (> 10) / SPbeta prophage-derived uncharacterized protein YopK
Function and homology information
Biological speciesBacillus subtilis (bacteria)
Bacillus phage SPbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMarina, A. / Gallego del Sol, F.
CitationJournal: Mol.Cell / Year: 2019
Title: Deciphering the Molecular Mechanism Underpinning Phage Arbitrium Communication Systems.
Authors: Gallego Del Sol, F. / Penades, J.R. / Marina, A.
History
DepositionSep 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Apr 17, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPBc2 prophage-derived uncharacterized protein YopK
B: SPBc2 prophage-derived uncharacterized protein YopK
C: DNA (43-MER)
D: DNA (43-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,78610
Polymers117,2164
Non-polymers5706
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-115 kcal/mol
Surface area46120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.157, 159.157, 245.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 386 / Label seq-ID: 1 - 386

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein SPBc2 prophage-derived uncharacterized protein YopK


Mass: 45372.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: yopK, BSU20860 / Production host: Escherichia coli (E. coli) / References: UniProt: O31927
#2: DNA chain DNA (43-MER)


Mass: 13270.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus phage SPbeta (virus)
#3: DNA chain DNA (43-MER)


Mass: 13199.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus phage SPbeta (virus)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: peg 400, hepes, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.2→133.61 Å / Num. obs: 79845 / % possible obs: 100 % / Redundancy: 26.8 % / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→133.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 15.857 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.184 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24647 4007 5 %RANDOM
Rwork0.2164 ---
obs0.21789 75807 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.708 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å2-0 Å20 Å2
2--1.56 Å2-0 Å2
3----3.12 Å2
Refinement stepCycle: 1 / Resolution: 2.2→133.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6366 1763 30 255 8414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0178486
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.76811808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6125.495333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.718151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0621526
X-RAY DIFFRACTIONr_chiral_restr0.130.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025737
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2274.1123088
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3966.1553857
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8954.4185396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.84354.00913304
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 25942 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 305 -
Rwork0.319 5537 -
obs--99.85 %
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)
10.36330.0690.13471.09390.16170.24820.0531-0.00350.0319-0.0513-0.04290.0533-0.0447-0.0149-0.01020.13350.0010.06060.04560.00170.033428.8195-9.155339.7175
20.12170.14020.10021.2686-0.03410.39660.04640.07610.00620.0778-0.00720.0620.02310.0358-0.03920.03310.00290.02360.0952-0.02250.029849.4115-9.71972.4186
30.11960.0427-0.29470.1356-0.2642.47070.0559-0.00320.0650.0480.00580.0046-0.21780.1185-0.06180.2208-0.01530.00360.17610.00120.259846.909722.693325.226
40.15020.0302-0.31870.096-0.11252.00050.0595-0.00760.0610.03610.02550.0099-0.1919-0.0133-0.0850.2415-0.0286-0.00120.17390.00160.27546.512622.764725.6063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 386
2X-RAY DIFFRACTION2B1 - 386
3X-RAY DIFFRACTION3C1 - 43
4X-RAY DIFFRACTION4D1 - 43

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