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- PDB-4bi4: Structure and function of amidase toxin - antitoxin combinations ... -

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Basic information

Entry
Database: PDB / ID: 4bi4
TitleStructure and function of amidase toxin - antitoxin combinations associated with the type VI secretion system of Serratia marcescens.
ComponentsSSP1 C50A MUTANT
KeywordsTOXIN
Function / homology
Function and homology information


endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsSrikannathasan, V. / English, G. / Bui, N.K. / Trunk, K. / Rourke, P.E.F.O. / Rao, V.A. / Vollmer, W. / 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SSP1 C50A MUTANT
B: SSP1 C50A MUTANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4403
Polymers36,3482
Non-polymers921
Water4,522251
1
A: SSP1 C50A MUTANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2662
Polymers18,1741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SSP1 C50A MUTANT


Theoretical massNumber of molelcules
Total (without water)18,1741
Polymers18,1741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.790, 64.590, 97.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SSP1 C50A MUTANT


Mass: 18173.807 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S4S1W2*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCES ARE NOT IN UNIPROT DATABASE

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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: 2.46 Å3/Da / Density % sol: 50 % / Description: 4BI3 IS ON HOLD FOR PUBLICATION
Crystal growpH: 5.5 / Details: 0.1M SODIUM CITRATE PH 5.5, 20% PEG 3000

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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: Sep 13, 2012
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→48.93 Å / Num. obs: 18726 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23
Reflection shellResolution: 2.21→2.26 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 8.1 / % possible all: 98.5

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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: 2.21→48.93 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.824 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24604 955 5.1 %RANDOM
Rwork0.19124 ---
obs0.194 17725 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.508 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.62 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.21→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 6 251 2820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022680
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9643619
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97723.982113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64515468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.537159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212025
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: 2.206→2.264 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 75 -
Rwork0.193 1128 -
obs--98.2 %

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