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- PDB-3sol: Crystal structure of the type 2 secretion system pilotin GspS -

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Basic information

Entry
Database: PDB / ID: 3sol
TitleCrystal structure of the type 2 secretion system pilotin GspS
ComponentsType II secretion pathway related protein
KeywordsPROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / PILOTIN / SECRETIN
Function / homology
Function and homology information


intracellular protein transport
Similarity search - Function
Chaperone lipoprotein PulS/OutS / Chaperone lipoprotein, PulS/OutS / Chaperone lipoprotein, PulS/OutS-like / PulS/OutS-like superfamily / Type II secretion system pilotin lipoprotein (PulS_OutS) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Type II secretion pathway related protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKorotkov, K.V. / Hol, W.G.J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of the pilotin from the enterohemorrhagic Escherichia coli type II secretion system.
Authors: Korotkov, K.V. / Hol, W.G.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Type II secretion pathway related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0155
Polymers10,8731
Non-polymers1424
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.350, 73.350, 70.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-200-

CL

21A-108-

CL

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Components

#1: Protein Type II secretion pathway related protein / Type II secretion protein


Mass: 10873.412 Da / Num. of mol.: 1 / Fragment: unp residues 39-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECO57PM13, etpO, GSPS, L7044 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BSV3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MG CHLORIDE, 0.1M TRIS-HCL, 30% PEG3350, pH 8.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2006
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→47.261 Å / Num. obs: 16858 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.384 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 24.39
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.952.4713064122598.8
1.95-23.73140721228100
2-2.065.23134401169100
2.06-2.127.1813281116599.9
2.12-2.198.63125531089100
2.19-2.279.49126201101100
2.27-2.3511.92119891035100
2.35-2.4513.0311487993100
2.45-2.5617.3911150960100
2.56-2.6821.5710672923100
2.68-2.8325.8510154873100
2.83-331.969576822100
3-3.2133.879042775100
3.21-3.4647.268295716100
3.46-3.7960.497731667100
3.79-4.2469.766975604100
4.24-4.978.416116528100
4.9-670.15167448100
6-8.4872.473972345100
8.4894.57205819299.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.26 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2004 / WRfactor Rwork: 0.1758 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8784 / SU B: 5.137 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1386 / SU Rfree: 0.1289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 426 4.6 %RANDOM
Rwork0.1901 ---
obs0.1916 9323 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 98.44 Å2 / Biso mean: 38.1188 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.33 Å20 Å2
2---0.65 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 4 61 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022754
X-RAY DIFFRACTIONr_bond_other_d0.0010.02540
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9711016
X-RAY DIFFRACTIONr_angle_other_deg0.82731303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.408590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44723.07739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1515145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7041510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
X-RAY DIFFRACTIONr_mcbond_it0.6251.5455
X-RAY DIFFRACTIONr_mcbond_other0.1551.5181
X-RAY DIFFRACTIONr_mcangle_it1.2322738
X-RAY DIFFRACTIONr_scbond_it2.1273299
X-RAY DIFFRACTIONr_scangle_it3.5754.5278
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 28 -
Rwork0.198 637 -
all-665 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 35.825 Å / Origin y: 39.565 Å / Origin z: 4.402 Å
111213212223313233
T0.209 Å20.073 Å2-0.0256 Å2-0.0757 Å2-0.0526 Å2--0.0958 Å2
L2.6232 °2-0.9155 °2-0.435 °2-4.241 °2-0.6801 °2--2.4922 °2
S0.0779 Å °0.2539 Å °-0.3955 Å °-0.4366 Å °-0.1281 Å °-0.1127 Å °0.5982 Å °0.2398 Å °0.0502 Å °

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