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- PDB-4bi8: Crystal structure of the type VI effector-immunity complex Ssp1-R... -

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Basic information

Entry
Database: PDB / ID: 4bi8
TitleCrystal structure of the type VI effector-immunity complex Ssp1-Rap1a from Serratia marcescens
Components
  • RAP1A
  • SSSP1
KeywordsTOXIN / PROTEIN RAP1A COMPLEX
Function / homology
Function and homology information


10k-s Protein, Hypothetical Protein A; Chain A - #40 / endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / 10k-s Protein, Hypothetical Protein A; Chain A / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) ...10k-s Protein, Hypothetical Protein A; Chain A - #40 / endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / 10k-s Protein, Hypothetical Protein A; Chain A / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSrikannathasan, V. / Coulthurst, S.J. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Basis for Type Vi Secreted Peptidoglycan Dl-Endopeptidase Function, Specificity and Neutralization in Serratia Marcescens
Authors: Srikannathasan, V. / English, G. / Bui, N.K. / Trunk, K. / Rourke, P.E.F.O. / Rao, V.A. / Vollmer, W. / Coulthurst, S.J. / Hunter, W.N.
History
DepositionApr 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAP1A
B: SSSP1


Theoretical massNumber of molelcules
Total (without water)29,7072
Polymers29,7072
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-9.7 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.470, 68.470, 92.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2036-

HOH

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Components

#1: Protein RAP1A


Mass: 11500.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10
Description: SEQUENCE DATA NOT AVAILABLE IN UNIPROT DATABASE
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S4S1W3*PLUS
#2: Protein SSSP1


Mass: 18205.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10
Description: SEQUENCE DATA NOT AVAILABLE IN UNIPROT DATABASE
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S4S1W1*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 12.5% PEG1K, 12.5% PEG3350 AND 12.5% MPD. 20% GLYCEROL AS A CRYO-PROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 HG / Detector: CCD / Date: Oct 23, 2012
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→49.92 Å / Num. obs: 17462 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 28.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 40.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 25.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 11.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BI3

4bi3


Resolution: 2→49.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.711 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22145 882 5.1 %RANDOM
Rwork0.1753 ---
obs0.1775 16564 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.653 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 0 192 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022115
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.9592857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9025259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17123.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76615367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8251510
X-RAY DIFFRACTIONr_chiral_restr0.0720.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211606
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 63 -
Rwork0.2 1097 -
obs--98.39 %
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)
11.19450.1863-0.40790.7150.27342.5765-0.03460.09090.0683-0.07850.00830.1233-0.3752-0.04730.02630.06950.006-0.01420.02580.01610.0587-25.593211.0522-31.4528
26.89530.24980.58615.23760.88723.9355-0.23750.03760.0442-0.06480.06170.3002-0.1063-0.26770.17570.03810.02210.00220.04870.00660.0269-32.59586.8743-23.3526
30.36090.04570.16161.0059-0.28380.975-0.0125-0.03050.0070.0635-0.028-0.0122-0.07810.1090.04060.0379-0.0066-0.00370.05650.00930.0372-17.59283.9011-21.8321
48.81020.8616-1.67379.9253-1.3039.8310.3009-0.32650.2920.528-0.1547-0.2018-0.25740.7423-0.14620.0518-0.0439-0.01950.1252-0.00030.0446-8.35430.8238-16.1443
58.7333.2603-4.94146.72336.900916.70690.32310.09380.1250.353-0.0798-0.05960.2051-0.3412-0.24330.0380.050.0290.17990.07030.1028-39.8186-3.92052.9437
61.08860.00190.15530.41060.19461.92160.0162-0.0160.00830.1992-0.04670.0083-0.13150.11110.03050.1313-0.03280.00460.02360.00530.0179-21.66480.6955-0.5563
71.1571.1370.18542.91071.61061.17880.1028-0.0437-0.08990.2839-0.0677-0.07520.1368-0.0316-0.03510.12640.0020.00150.02140.03220.0495-29.4923-15.1159-1.754
80.94790.3063-0.79321.14660.23061.5990.03330.09130.0013-0.0164-0.090.14120.0025-0.07890.05670.04830.01350.00990.0366-0.00030.0461-33.216-10.4211-10.2313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 49
2X-RAY DIFFRACTION2A50 - 57
3X-RAY DIFFRACTION3A58 - 115
4X-RAY DIFFRACTION4A116 - 123
5X-RAY DIFFRACTION5B1 - 7
6X-RAY DIFFRACTION6B8 - 77
7X-RAY DIFFRACTION7B78 - 111
8X-RAY DIFFRACTION8B112 - 163

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