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- PDB-8a9w: Crystal structure of PulL C-ter domain -

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Basic information

Entry
Database: PDB / ID: 8a9w
TitleCrystal structure of PulL C-ter domain
ComponentsType II secretion system protein L
KeywordsSTRUCTURAL PROTEIN / Type II Secretion System / Assembly platform / Klebsiella oxytoca / Ferredoxin-like domain
Function / homology:
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 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
DepositionJun 29, 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 1.2Apr 12, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 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
A: Type II secretion system protein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8813
Polymers8,6891
Non-polymers1922
Water30617
1
A: Type II secretion system protein L
hetero molecules

A: Type II secretion system protein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7626
Polymers17,3782
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555-x+1/2,y,-z1
Buried area1240 Å2
ΔGint-21 kcal/mol
Surface area8610 Å2
Unit cell
Length a, b, c (Å)80.300, 80.300, 80.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Type II secretion system protein L / T2SS protein L


Mass: 8688.874 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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.5 M LiSO4 and 15%w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.895→56.781 Å / Num. obs: 7013 / % possible obs: 100 % / Redundancy: 39.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.012 / Rrim(I) all: 0.074 / Net I/σ(I): 30.3
Reflection shellResolution: 1.895→1.927 Å / Rmerge(I) obs: 1.814 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 356 / CC1/2: 0.782 / Rpim(I) all: 0.291 / Rrim(I) all: 1.837

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Processing

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

Resolution: 1.895→56.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.681 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27651 746 10.6 %RANDOM
Rwork0.24076 ---
obs0.24464 6267 100 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.178 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.895→56.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms579 0 10 17 606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.018589
X-RAY DIFFRACTIONr_bond_other_d0.0010.02588
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.894789
X-RAY DIFFRACTIONr_angle_other_deg1.0062.6691336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.734573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04919.73738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.06715110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.337159
X-RAY DIFFRACTIONr_chiral_restr0.0750.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02148
X-RAY DIFFRACTIONr_mcbond_it30.8745.564298
X-RAY DIFFRACTIONr_mcbond_other30.8125.536296
X-RAY DIFFRACTIONr_mcangle_it33.3918.147369
X-RAY DIFFRACTIONr_mcangle_other33.4168.145369
X-RAY DIFFRACTIONr_scbond_it33.8987.199291
X-RAY DIFFRACTIONr_scbond_other33.4877.194284
X-RAY DIFFRACTIONr_scangle_other33.3949.913409
X-RAY DIFFRACTIONr_long_range_B_refined37.38966.873608
X-RAY DIFFRACTIONr_long_range_B_other37.43366.907607
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 51 -
Rwork0.294 440 -
obs--100 %

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