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- PDB-4k0u: Pilotin/secretin peptide Complex -

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Basic information

Entry
Database: PDB / ID: 4k0u
TitlePilotin/secretin peptide Complex
Components
  • Lipoprotein OutS
  • Type II secretion system protein D
KeywordsPROTEIN TRANSPORT / Type II secretion system / pilotin-secretin complex / Outer membrane / Dickeya dadantii
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / 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) / Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. ...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) / Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Secretin OutD / Pilotin OutS
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRehman, S. / Pickersgill, R.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Anatomy of secretin binding to the Dickeya dadantii type II secretion system pilotin.
Authors: Rehman, S. / Gu, S. / Shevchik, V.E. / Pickersgill, R.W.
#1: Journal: Plos Pathog. / Year: 2012
Title: Structural and functional insights into the pilotin-secretin complex of the type II secretion system.
Authors: Gu, S. / Rehman, S. / Wang, X. / Shevchik, V.E. / Pickersgill, R.W.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 15, 2013ID: 3UYM
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein OutS
B: Type II secretion system protein D


Theoretical massNumber of molelcules
Total (without water)13,4422
Polymers13,4422
Non-polymers00
Water25214
1
A: Lipoprotein OutS
B: Type II secretion system protein D

A: Lipoprotein OutS
B: Type II secretion system protein D


Theoretical massNumber of molelcules
Total (without water)26,8844
Polymers26,8844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-11 kcal/mol
Surface area6040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.602, 53.602, 142.441
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

#1: Protein Lipoprotein OutS


Mass: 11591.064 Da / Num. of mol.: 1 / Fragment: UNP residues 28-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: Dda3937_02411, outS, OutS Dda3937_02411 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01567
#2: Protein/peptide Type II secretion system protein D / T2SS protein D / General secretion pathway protein D / Pectic enzymes secretion protein OutD


Mass: 1850.983 Da / Num. of mol.: 1 / Fragment: UNP residues 693-705 / Source method: obtained synthetically
Details: Synthetic peptide C-terminal OutD (Dickeya dadantii 3937)
Source: (synth.) Dickeya dadantii (bacteria) / References: UniProt: Q01565
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES ARG B 1 AND ASP B 15 WERE ADDED TO THE SYNTHETIC PEPTIDE TO AID SOLUBILITY

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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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% PEG 400, 0.1M HEPES sodium, 2M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.15→47.48 Å / Num. obs: 7209 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 9.1
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1009 / Rsym value: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UTK

3utk


Resolution: 2.15→46.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.019 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.237 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27597 367 5.1 %RANDOM
Rwork0.20994 ---
all0.21298 7209 --
obs0.21298 6790 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.629 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å21.04 Å2-0 Å2
2--1.04 Å2-0 Å2
3----3.37 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 0 14 875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02875
X-RAY DIFFRACTIONr_bond_other_d0.0010.02834
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9631185
X-RAY DIFFRACTIONr_angle_other_deg0.8313.0021913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50424.3941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.268157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 24 -
Rwork0.3 481 -
obs-8147 100 %

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