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- PDB-6xtd: Rhs1-CT in complex with cognate immunity protein RhsI1 -

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Basic information

Entry
Database: PDB / ID: 6xtd
TitleRhs1-CT in complex with cognate immunity protein RhsI1
Components
  • Putative deoxyribonuclease RhsA
  • Secreted protein
KeywordsANTIMICROBIAL PROTEIN / Type VI secretion system / Anti-bacterial toxin / Type VI effector / ANTIMICROBIAL PROTEIN Effector and immunity complex / RHS protein
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds / hydrolase activity
Similarity search - Function
Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / PAAR motif / PAAR motif / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / :
Similarity search - Domain/homology
BROMIDE ION / Putative deoxyribonuclease RhsA
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsHagan, M.R. / Hunter, B. / Coulthurst, S.
Funding support1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)
CitationJournal: To Be Published
Title: Rhs1-CT in complex with cognate immunity protein RhsI1
Authors: Hagan, M. / Coulthurst, S.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / database_2 / entity / entity_name_com / entity_poly / entity_src_gen / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_poly.pdbx_strand_id / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_status.pdb_format_compatible / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative deoxyribonuclease RhsA
B: Secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6029
Polymers35,9142
Non-polymers6897
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-11 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.655, 44.108, 46.807
Angle α, β, γ (deg.)101.202, 96.126, 114.149
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative deoxyribonuclease RhsA / Rhs1-CT


Mass: 17219.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: rhsA_2, PWN146_02504 / Plasmid: pSC962 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1C3HFI3, Hydrolases; Acting on ester bonds
#2: Protein Secreted protein / RhsI1


Mass: 18694.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: pSC962 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5 25% PEG 3350

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.3→35.418 Å / Num. obs: 65672 / % possible obs: 96.1 % / Redundancy: 10.2 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.222 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3188 / CC1/2: 0.808 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→35.418 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.119 / SU B: 1.844 / SU ML: 0.033 / Average fsc free: 0.9458 / Average fsc work: 0.9565 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1652 3327 5.07 %
Rwork0.1212 62295 -
all0.123 --
obs-65622 96.05 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0.26 Å2-0.272 Å2
2--0.315 Å2-0.412 Å2
3---0.776 Å2
Refinement stepCycle: LAST / Resolution: 1.3→35.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 20 392 2765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0132521
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172325
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.6523422
X-RAY DIFFRACTIONr_angle_other_deg1.6081.5845410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36521.618136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31915444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.271518
X-RAY DIFFRACTIONr_chiral_restr0.1250.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022860
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02578
X-RAY DIFFRACTIONr_nbd_refined0.2290.2500
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.22252
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21228
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2820.216
X-RAY DIFFRACTIONr_nbd_other0.2640.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.223
X-RAY DIFFRACTIONr_mcbond_it3.1651.6671214
X-RAY DIFFRACTIONr_mcbond_other3.1141.6631213
X-RAY DIFFRACTIONr_mcangle_it3.62.5081523
X-RAY DIFFRACTIONr_mcangle_other3.62.5121524
X-RAY DIFFRACTIONr_scbond_it5.5362.1591307
X-RAY DIFFRACTIONr_scbond_other5.5352.1591308
X-RAY DIFFRACTIONr_scangle_it5.8723.0361886
X-RAY DIFFRACTIONr_scangle_other5.8713.0361887
X-RAY DIFFRACTIONr_lrange_it6.01522.3573074
X-RAY DIFFRACTIONr_lrange_other6.01422.363075
X-RAY DIFFRACTIONr_rigid_bond_restr11.02534846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.2742280.224462X-RAY DIFFRACTION93.3148
1.334-1.370.2692150.1984458X-RAY DIFFRACTION94.1757
1.37-1.410.2242250.1754292X-RAY DIFFRACTION94.3992
1.41-1.4530.2342100.1624186X-RAY DIFFRACTION94.6598
1.453-1.5010.2282080.1494053X-RAY DIFFRACTION94.8998
1.501-1.5540.181990.1163944X-RAY DIFFRACTION95.1976
1.554-1.6120.1731890.1053845X-RAY DIFFRACTION95.4341
1.612-1.6780.1821930.1023688X-RAY DIFFRACTION95.6382
1.678-1.7520.1842070.13518X-RAY DIFFRACTION96.0052
1.752-1.8380.1721740.0933406X-RAY DIFFRACTION96.496
1.838-1.9370.1521790.0953229X-RAY DIFFRACTION97.2048
1.937-2.0540.1581610.1053107X-RAY DIFFRACTION97.2619
2.054-2.1960.1431900.1062872X-RAY DIFFRACTION97.3609
2.196-2.3710.1291570.1032684X-RAY DIFFRACTION98.067
2.371-2.5970.1591450.1052518X-RAY DIFFRACTION98.157
2.597-2.9020.1491220.1162264X-RAY DIFFRACTION98.6358
2.902-3.3490.1561200.1192014X-RAY DIFFRACTION98.8879
3.349-4.0960.128820.1151713X-RAY DIFFRACTION99.1165
4.096-5.7680.17860.1431311X-RAY DIFFRACTION99.5014
5.768-35.4180.235370.19732X-RAY DIFFRACTION99.354

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