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- PDB-8ab1: Crystal structure of the PulL-PulM C-terminal domain heterocomplex -

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Basic information

Entry
Database: PDB / ID: 8ab1
TitleCrystal structure of the PulL-PulM C-terminal domain heterocomplex
Components
  • (Type II secretion system protein M) x 2
  • Type II secretion system protein L
KeywordsSTRUCTURAL PROTEIN / Type II Secretion System / Assembly platform / Klebsiella oxytoca / Ferredoxin-like domain
Function / homologyGeneral secretion pathway protein M, EpsM / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta / : / :
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsDazzoni, R. / Li, Y. / Lopez-Castilla, A. / Brier, S. / Mechaly, A. / Cordier, F. / Haouz, A. / Nilges, M. / Francetic, O. / Bardiaux, B. / Izadi-Pruneyre, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)19-CE11-0020-01 France
CitationJournal: Structure / Year: 2023
Title: Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system.
Authors: Dazzoni, R. / Li, Y. / Lopez-Castilla, A. / Brier, S. / Mechaly, A. / Cordier, F. / Haouz, A. / Nilges, M. / Francetic, O. / Bardiaux, B. / Izadi-Pruneyre, N.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Type II secretion system protein M
C: Type II secretion system protein M
D: Type II secretion system protein M
E: Type II secretion system protein L


Theoretical massNumber of molelcules
Total (without water)33,2314
Polymers33,2314
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-14 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.899, 117.899, 110.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Type II secretion system protein M / T2SS protein M / General secretion pathway protein M


Mass: 8261.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DVB85_16620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B2TA77
#2: Protein Type II secretion system protein M / T2SS protein M / General secretion pathway protein M


Mass: 7948.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DVB85_16620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B2TA77
#3: Protein Type II secretion system protein L / T2SS protein L


Mass: 8759.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: gspL, DVB85_16625 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B2T914
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0%w/v PEG 3350, 0.2M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.77→102.104 Å / Num. obs: 11982 / % possible obs: 100 % / Redundancy: 38.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.016 / Rrim(I) all: 0.101 / Net I/σ(I): 25
Reflection shellResolution: 2.77→2.819 Å / Redundancy: 41.1 % / Rmerge(I) obs: 1.982 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 586 / CC1/2: 0.834 / Rpim(I) all: 0.311 / Rrim(I) all: 2.007 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
AutoProcessdata scaling
AutoProcessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NMR models

Resolution: 2.77→102.1 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.929 / SU B: 35.359 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R: 0.827 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29278 581 4.8 %RANDOM
Rwork0.27173 ---
obs0.27277 11401 99.94 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å2-0 Å2
2---0.19 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.77→102.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 21 2347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0182357
X-RAY DIFFRACTIONr_bond_other_d0.0020.0192362
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.8763208
X-RAY DIFFRACTIONr_angle_other_deg1.1482.6955377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4775304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53920.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31515395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.551525
X-RAY DIFFRACTIONr_chiral_restr0.1140.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
X-RAY DIFFRACTIONr_mcbond_it0.9855.8331228
X-RAY DIFFRACTIONr_mcbond_other0.9855.8341227
X-RAY DIFFRACTIONr_mcangle_it1.7088.7471528
X-RAY DIFFRACTIONr_mcangle_other1.7088.7471529
X-RAY DIFFRACTIONr_scbond_it0.8615.9561127
X-RAY DIFFRACTIONr_scbond_other0.8615.9561128
X-RAY DIFFRACTIONr_scangle_other1.4698.8721680
X-RAY DIFFRACTIONr_long_range_B_refined4.90670.3142552
X-RAY DIFFRACTIONr_long_range_B_other4.86170.2242550
LS refinement shellResolution: 2.771→2.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 40 -
Rwork0.32 812 -
obs--99.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.0268-3.41030.40489.90112.74277.7729-0.1555-1.01860.42070.8379-0.06080.44020.1653-0.29910.21630.0769-0.02840.06620.186-0.11610.212451.115-52.8-21.665
29.6769-7.04375.667313.96820.13618.8731-0.7901-0.5818-0.74420.92670.11772.3821-0.6591-2.07150.67230.72020.50870.79141.34740.02511.6209-1.898-26.912-3.36
38.0121-1.1089-3.62848.84431.03254.9128-0.4185-0.4145-0.72010.54690.19930.52580.5589-0.07750.21910.1171-0.00820.09280.10390.04370.154831.08-49.157-15.014
411.0044-3.3091-1.21759.75440.729810.3662-0.17580.1906-0.44390.3635-0.02252.18620.0706-1.76230.19830.24180.07710.28140.70130.01520.995212.913-38.55-12.384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 79
2X-RAY DIFFRACTION2C6 - 79
3X-RAY DIFFRACTION3D3 - 79
4X-RAY DIFFRACTION4E7 - 86

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