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- PDB-5wec: Structure of an alternative pilotin from the type II secretion sy... -

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Basic information

Entry
Database: PDB / ID: 5wec
TitleStructure of an alternative pilotin from the type II secretion system of Vibrio cholerae
ComponentsLipoprotein
KeywordsPROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / PILOTIN / SECRETIN / VC_1064 / EXSB
Function / homology: / Type 3 secretion system pilotin / Type III secretion system lipoprotein chaperone (YscW) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.563 Å
AuthorsWilliamson, Z.A. / Reed, R.W. / Korotkov, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: To Be Published
Title: Structure and function of a new pilotin from the type II secretion system of Vibrio cholerae
Authors: Williamson, Z.A. / Reed, R.W. / Korotkov, K.V.
History
DepositionJul 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein
B: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)25,7512
Polymers25,7512
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-9 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.890, 60.120, 73.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipoprotein


Mass: 12875.714 Da / Num. of mol.: 2 / Fragment: UNP residues 30-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A0582 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A0A0H3AJJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48 % / Description: rectangular prism
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES PH 6.5, 10% PEG6000, FINAL PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2017
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→46.619 Å / Num. obs: 34736 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.347 % / Biso Wilson estimate: 18.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.108 / Χ2: 0.938 / Net I/σ(I): 10.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.56-1.63.980.9541.3820820.5211.09282.2
1.6-1.656.260.9432.0524830.7231.02799.1
1.65-1.76.6550.7842.6624580.80.85100
1.7-1.756.5870.6273.323480.8630.68199.9
1.75-1.86.4870.4844.0823180.9180.52699.8
1.8-1.876.1280.3645.2122150.9410.39899.6
1.87-1.946.7620.2597.0521570.9730.281100
1.94-2.026.6930.189.4320550.9870.19599.9
2.02-2.116.6010.14411.3120130.9890.15799.9
2.11-2.216.2550.12911.8818860.990.14199.6
2.21-2.336.5390.11113.9918240.9920.1299.9
2.33-2.476.7710.10315.1417200.9930.111100
2.47-2.646.680.09416.1216350.9950.10299.9
2.64-2.856.2310.08317.4115100.9940.0999.9
2.85-3.136.6580.07120.8514060.9950.07799.9
3.13-3.56.730.06823.1312760.9960.07499.8
3.5-4.046.3470.06823.8111450.9950.07499.8
4.04-4.946.290.06824.369720.9940.07499.6
4.94-6.996.3270.06823.687770.9950.074100
6.99-46.6195.750.0624.034560.9960.06699.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEVERSION Jun 1, 2017 BUILT=20170601data scaling
PHASER2.8.0phasing
PHENIX1.12rc1_2815refinement
PDB_EXTRACT3.22data extraction
XDSVERSION Jun 1, 2017 BUILT=20170601data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.563→46.619 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 3151 4.82 %RANDON SELECTION
Rwork0.1822 ---
obs0.1834 34735 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.18 Å2 / Biso mean: 26.6838 Å2 / Biso min: 11.8 Å2
Refinement stepCycle: final / Resolution: 1.563→46.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 0 235 1983
Biso mean---32 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041792
X-RAY DIFFRACTIONf_angle_d0.7252439
X-RAY DIFFRACTIONf_chiral_restr0.055290
X-RAY DIFFRACTIONf_plane_restr0.005312
X-RAY DIFFRACTIONf_dihedral_angle_d9.7011096
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.563-1.58640.3187770.32781770184764
1.5864-1.61120.35121240.31582714283897
1.6112-1.63760.27681430.2872702284599
1.6376-1.66580.25951380.267627782916100
1.6658-1.69610.28881180.258827522870100
1.6961-1.72870.28311560.249227662922100
1.7287-1.7640.23431360.23362764290099
1.764-1.80240.25131490.2327132862100
1.8024-1.84430.25691520.23472723287599
1.8443-1.89040.30661270.209227952922100
1.8904-1.94160.24471390.201427622901100
1.9416-1.99870.18971370.18092743288099
1.9987-2.06320.19791590.168227212880100
2.0632-2.13690.19061390.174827582897100
2.1369-2.22250.2331170.17352746286399
2.2225-2.32360.17981260.166227922918100
2.3236-2.44610.19841470.166327662913100
2.4461-2.59940.17131460.186327402886100
2.5994-2.80010.22231650.17427512916100
2.8001-3.08180.1981760.176627102886100
3.0818-3.52760.21781330.165427832916100
3.5276-4.44390.19691150.152327532868100
4.4439-46.63950.15561320.161527802912100

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