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- PDB-6xfj: Crystal structure of the type III secretion pilotin InvH -

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Basic information

Entry
Database: PDB / ID: 6xfj
TitleCrystal structure of the type III secretion pilotin InvH
ComponentsType 3 secretion system pilotinType three secretion system
KeywordsPROTEIN TRANSPORT / pilotin / chaperone / type III secretion / dimer
Function / homologyInvH outer membrane lipoprotein / InvH outer membrane lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / : / SPI-1 type 3 secretion system pilotin
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsMajewski, D.D. / Okon, M. / Heinkel, F. / Robb, C.S. / Vuckovic, M. / McIntosh, L.P. / Strynadka, N.C.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Structure / Year: 2021
Title: Characterization of the Pilotin-Secretin Complex from the Salmonella enterica Type III Secretion System Using Hybrid Structural Methods.
Authors: Majewski, D.D. / Okon, M. / Heinkel, F. / Robb, C.S. / Vuckovic, M. / McIntosh, L.P. / Strynadka, N.C.J.
History
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 3 secretion system pilotin
B: Type 3 secretion system pilotin
C: Type 3 secretion system pilotin
D: Type 3 secretion system pilotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,27439
Polymers37,8154
Non-polymers2,46035
Water7,296405
1
A: Type 3 secretion system pilotin
B: Type 3 secretion system pilotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,14920
Polymers18,9072
Non-polymers1,24118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-142 kcal/mol
Surface area8540 Å2
MethodPISA
2
C: Type 3 secretion system pilotin
D: Type 3 secretion system pilotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,12619
Polymers18,9072
Non-polymers1,21817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-140 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.503, 53.183, 56.851
Angle α, β, γ (deg.)107.690, 97.200, 95.950
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Type 3 secretion system pilotin / Type three secretion system / Invasion lipoprotein invH


Mass: 9453.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: invH, sctG, STM2900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CL43
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 303 K / Method: microbatch / pH: 4.6
Details: 80 mM cadmium chloride, 20% PEG 300, 400 mM NaCl, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→44.36 Å / Num. obs: 82540 / % possible obs: 94.5 % / Redundancy: 3.9 % / CC1/2: 0.998 / Net I/σ(I): 11.1
Reflection shellResolution: 1.2→1.24 Å / Num. unique obs: 7937 / CC1/2: 0.681

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→44.36 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.969 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.168 4112 5 %RANDOM
Rwork0.1323 ---
obs0.1341 78427 94.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.77 Å2 / Biso mean: 14.865 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20.15 Å21.11 Å2
2---0.37 Å20.74 Å2
3---1.21 Å2
Refinement stepCycle: final / Resolution: 1.2→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 37 405 2903
Biso mean--21.28 31.02 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132671
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182427
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.6463618
X-RAY DIFFRACTIONr_angle_other_deg1.7041.5735738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9955347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26224.82139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02615535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.917159
X-RAY DIFFRACTIONr_chiral_restr0.1160.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023010
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02517
X-RAY DIFFRACTIONr_rigid_bond_restr7.38135098
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 286 -
Rwork0.25 5605 -
all-5891 -
obs--91.12 %

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