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- PDB-7q0n: Arbitrium receptor from Katmira phage -

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Basic information

Entry
Database: PDB / ID: 7q0n
TitleArbitrium receptor from Katmira phage
Components
  • (DNA (45-MER)) x 2
  • Arbitrium receptor
KeywordsDNA BINDING PROTEIN / Arbitrium
Function / homologyDNA / DNA (> 10) / Arbitrium receptor
Function and homology information
Biological speciesBacillaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGallego del Sol, F. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish National Research Council Spain
CitationJournal: Nat Commun / Year: 2022
Title: Insights into the mechanism of action of the arbitrium communication system in SPbeta phages.
Authors: Gallego Del Sol, F. / Quiles-Puchalt, N. / Brady, A. / Penades, J.R. / Marina, A.
History
DepositionOct 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: Arbitrium receptor
B: Arbitrium receptor
C: DNA (45-MER)
D: DNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,90211
Polymers118,2294
Non-polymers6727
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-188 kcal/mol
Surface area47190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.719, 39.866, 143.015
Angle α, β, γ (deg.)90.000, 100.490, 90.000
Int Tables number4
Space group name H-MP1211
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: MET / End label comp-ID: MET / 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 Arbitrium receptor


Mass: 45261.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillaceae (bacteria) / Gene: aimR, Goe11_c00800 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G5CHT1
#2: DNA chain DNA (45-MER)


Mass: 13850.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillaceae (bacteria)
#3: DNA chain DNA (45-MER)


Mass: 13854.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillaceae (bacteria)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 400, Sodium acetate, Litium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.5→140.627 Å / Num. all: 50324 / Num. obs: 50324 / % possible obs: 96.7 % / Redundancy: 6.4 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Rsym value: 0.098 / Net I/av σ(I): 4.4 / Net I/σ(I): 9.2 / Num. measured all: 320049
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.645.31.5470.53215860370.731.7221.547181.1
2.64-2.86.21.0190.74317169640.4431.1141.0191.798.2
2.8-2.996.90.6491.24602166540.2640.7010.6492.899.7
2.99-3.236.70.2822.54199562390.1170.3060.282599.5
3.23-3.546.70.1544.43844757340.0650.1680.1548.799.6
3.54-3.956.50.1066.23393652390.0450.1150.10612.999.7
3.95-4.566.50.0748.22984246050.0320.0810.07418.899.5
4.56-5.596.20.0679.22470639640.0290.0730.06719.299.6
5.59-7.916.30.0619.71945731130.0260.0670.06120.199.7
7.91-65.2515.80.0519.31031617750.0230.0560.05128.698.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HP7

6hp7


Resolution: 2.5→65.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 30.838 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.393 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2549 5.1 %RANDOM
Rwork0.2018 ---
obs0.2043 47746 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 210.9 Å2 / Biso mean: 84.307 Å2 / Biso min: 44.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20.42 Å2
2--3.42 Å20 Å2
3----1.91 Å2
Refinement stepCycle: final / Resolution: 2.5→65.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6356 1845 35 49 8285
Biso mean--141.85 70.91 -
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138598
X-RAY DIFFRACTIONr_bond_other_d0.0050.0167244
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.66511967
X-RAY DIFFRACTIONr_angle_other_deg1.3031.57716792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55424.444360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.649151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.4841525
X-RAY DIFFRACTIONr_chiral_restr0.1110.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028423
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021824
Refine LS restraints NCS

Ens-ID: 1 / Number: 13226 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 130 -
Rwork0.38 2648 -
all-2778 -
obs--73.61 %
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)
13.1532-1.36851.29430.7107-0.53891.83440.1510.3473-0.2612-0.0657-0.15130.17570.0353-0.31820.00030.0623-0.00730.05090.3346-0.08070.144615.2064-0.042754.9532
21.31530.08680.82060.59051.04233.4790.01910.4330.0704-0.2211-0.1950.0125-0.2717-0.18520.17580.16080.09190.09990.4060.06040.149147.66275.420426.1447
36.778-1.7757-5.69560.50031.47144.83220.24570.89980.2448-0.1101-0.1005-0.0555-0.0763-0.749-0.14520.37920.10650.20421.2169-0.09230.42518.59622.967914.6446
46.3614-1.8744-6.13840.58581.83025.9824-0.05571.1316-0.1236-0.0178-0.21540.06550.1523-0.98770.2710.3960.10890.2631.2831-0.07590.50528.61142.247814.6731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 386
2X-RAY DIFFRACTION2B1 - 386
3X-RAY DIFFRACTION3C1 - 45
4X-RAY DIFFRACTION4D1 - 45

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