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- PDB-6hp5: ARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE -

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Basic information

Entry
Database: PDB / ID: 6hp5
TitleARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE
Components
  • GLY-MET-PRO-ARG-GLY-ALA
  • SPBc2 prophage-derived uncharacterized protein YopK
KeywordsDNA BINDING PROTEIN / Arbitrium peptide receptor / SPbeta phage
Function / homology: / SPbeta prophage-derived uncharacterized protein YopK
Function and homology information
Biological speciesBacillus subtilis (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 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 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPBc2 prophage-derived uncharacterized protein YopK
B: SPBc2 prophage-derived uncharacterized protein YopK
C: GLY-MET-PRO-ARG-GLY-ALA
D: GLY-MET-PRO-ARG-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,15523
Polymers93,3304
Non-polymers1,82519
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-258 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.340, 94.340, 249.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 386
2010B1 - 386

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Components

#1: Protein SPBc2 prophage-derived uncharacterized protein YopK


Mass: 46076.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yopK, BSU20860 / Production host: Escherichia coli (E. coli) / References: UniProt: O31927
#2: Protein/peptide GLY-MET-PRO-ARG-GLY-ALA


Mass: 588.701 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: peg 3500, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.28→88.262 Å / Num. obs: 52488 / % possible obs: 100 % / Redundancy: 17.9 % / Net I/σ(I): 14.8
Reflection shellResolution: 2.28→2.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→88.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 15.005 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22577 2646 5 %RANDOM
Rwork0.19044 ---
obs0.19222 49841 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.28→88.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 95 163 6704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9958950
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4155782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.35925.389334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.491151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.211528
X-RAY DIFFRACTIONr_chiral_restr0.1240.2986
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024900
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_it2.5475.4963137
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.888.2353916
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1855.9713509
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.8674.3549822
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: 26400 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 184 -
Rwork0.294 3627 -
obs--100 %
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)
10.1109-0.08420.05020.0742-0.07060.3684-0.02620.0219-0.02010.0247-0.01190.0052-0.0522-0.06420.03810.01760.0141-0.00370.0373-0.01530.014939.916432.542839.6624
20.2703-0.1147-0.0680.10560.00870.05790.01390.0067-0.0202-0.0235-0.00170.0150.00330.0006-0.01210.02220.01460.00430.01350.00480.019519.119815.151173.3153
300000000000000-00.0226000.022600.0226000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 386
2X-RAY DIFFRACTION2B1 - 386

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