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- PDB-3utk: Structure of the pilotin of the type II secretion system -

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Basic information

Entry
Database: PDB / ID: 3utk
TitleStructure of the pilotin of the type II secretion system
ComponentsLipoprotein outS
KeywordsPROTEIN TRANSPORT / Nested (perpendicular) alpha-helical hairpins / PILOT PROTEIN
Function / homology
Function and homology information


intracellular protein transport / cell outer membrane / protein processing
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
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsRehman, S. / Pickersgill, R.W.
CitationJournal: TO BE PUBLISHED
Title: Structure of the pilotin of the type II secretion system
Authors: Gu, S. / Rehman, S. / Wang, X. / Shevchik, V.E. / Pickersgill, R.W.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein outS
B: Lipoprotein outS


Theoretical massNumber of molelcules
Total (without water)28,6992
Polymers28,6992
Non-polymers00
Water3,513195
1
A: Lipoprotein outS


Theoretical massNumber of molelcules
Total (without water)14,3491
Polymers14,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoprotein outS


Theoretical massNumber of molelcules
Total (without water)14,3491
Polymers14,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 53.095, 98.735
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 Lipoprotein outS


Mass: 14349.450 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: outS, Dda3937_02411 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q01567
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 2% PEG 400, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2010 / Details: Silicon monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 1.65→46.78 Å / Num. all: 32767 / Num. obs: 32440 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.2 / Rsym value: 0.2 / Net I/σ(I): 6.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4652 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→46.762 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1533 4.89 %
Rwork0.1966 --
obs0.1992 31358 97.5 %
all-32162 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.19 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1805 Å2-0 Å2-0 Å2
2---1.9179 Å20 Å2
3----5.3699 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 195 1657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061490
X-RAY DIFFRACTIONf_angle_d0.9182021
X-RAY DIFFRACTIONf_dihedral_angle_d12.483561
X-RAY DIFFRACTIONf_chiral_restr0.057237
X-RAY DIFFRACTIONf_plane_restr0.004263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.7090.33351180.23792816X-RAY DIFFRACTION93
1.709-1.77740.27161290.20292888X-RAY DIFFRACTION95
1.7774-1.85830.25561450.18072863X-RAY DIFFRACTION96
1.8583-1.95630.26541700.19062845X-RAY DIFFRACTION95
1.9563-2.07880.24961570.18682996X-RAY DIFFRACTION98
2.0788-2.23940.25181590.18872975X-RAY DIFFRACTION99
2.2394-2.46470.24031560.17893030X-RAY DIFFRACTION99
2.4647-2.82130.20451740.18273053X-RAY DIFFRACTION100
2.8213-3.55440.24451600.19613114X-RAY DIFFRACTION100
3.5544-46.78120.2671650.21193245X-RAY DIFFRACTION100

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