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- PDB-7prg: Joint X-ray/neutron room temperature structure of perdeuterated L... -

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Basic information

Entry
Database: PDB / ID: 7prg
TitleJoint X-ray/neutron room temperature structure of perdeuterated LecB lectin in complex with perdeuterated fucose
ComponentsFucose-binding lectin
KeywordsSUGAR BINDING PROTEIN / lectin / complex
Function / homologyLectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / carbohydrate binding / alpha-L-fucopyranose / Fucose-binding lectin
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGajdos, L. / Blakeley, M.P. / Haertlein, M. / Forsyth, T.V. / Devos, J.M. / Imberty, A.
Funding support France, 1items
OrganizationGrant numberCountry
Institut Laue-Langevin France
CitationJournal: Nat Commun / Year: 2022
Title: Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding.
Authors: Gajdos, L. / Blakeley, M.P. / Haertlein, M. / Forsyth, V.T. / Devos, J.M. / Imberty, A.
History
DepositionSep 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / exptl / pdbx_initial_refinement_model / refine / reflns / reflns_shell
Item: _diffrn_detector.pdbx_collection_date / _diffrn_detector.type ..._diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type / _exptl.crystals_number / _refine.pdbx_diffrn_id / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53717
Polymers47,4644
Non-polymers1,07313
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.900, 73.870, 55.003
Angle α, β, γ (deg.)90.000, 94.580, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069Q9V4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris/DCl, pD 7.1, 20% (w/v) PEG 4000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SEALED TUBEXenocs GeniX 3D Cu HF11.5418
NUCLEAR REACTORILL LADI III22.8-3.8
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATESep 16, 2020
LADI III2IMAGE PLATEAug 18, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
22.81
33.81
Reflection

Biso Wilson estimate: 12.85 Å2 / Entry-ID: 7PRG

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)Rpim(I) all
1.85-333485596.6710.097111.3
1.9-432447873.83.725.510.9
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-IDRpim(I) all
1.85-1.8915860.851
1.9-2.084860217

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
Cootmodel building
SCALAdata scaling
PHASERphasing
Refinement

SU ML: 0.1284 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 12.8624 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 1GZT

1gzt

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.85-27.41X-RAY DIFFRACTION21.520.14190.10420.106117363299834734596.2211.36
1.9-42.92NEUTRON DIFFRACTION0.24610.19140.19411195242834.9272.842
Refine analyzeLuzzati coordinate error free: 1 Å
Refinement stepCycle: LAST / Resolution: 1.85→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 57 364 3729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01017941
X-RAY DIFFRACTIONf_angle_d1.269313360
X-RAY DIFFRACTIONf_chiral_restr0.074636
X-RAY DIFFRACTIONf_plane_restr0.00681199
X-RAY DIFFRACTIONf_dihedral_angle_d17.88922841
NEUTRON DIFFRACTIONf_bond_d0.01017941
NEUTRON DIFFRACTIONf_angle_d1.269313360
NEUTRON DIFFRACTIONf_chiral_restr0.074636
NEUTRON DIFFRACTIONf_plane_restr0.00681199
NEUTRON DIFFRACTIONf_dihedral_angle_d17.88922841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.20921160.1752101X-RAY DIFFRACTION73.68
1.9-1.970.16481250.12552596X-RAY DIFFRACTION90.64
1.97-2.040.15071500.10772766X-RAY DIFFRACTION97.36
2.04-2.120.16411650.10922790X-RAY DIFFRACTION98.76
2.12-2.210.14461350.10032825X-RAY DIFFRACTION99.06
2.21-2.330.13751710.09582791X-RAY DIFFRACTION99.4
2.33-2.480.13551400.09682837X-RAY DIFFRACTION99.67
2.48-2.670.16011450.10612867X-RAY DIFFRACTION99.83
2.67-2.940.16971690.11452855X-RAY DIFFRACTION100
2.94-3.360.14861420.11092850X-RAY DIFFRACTION100
3.36-4.230.11951340.08982892X-RAY DIFFRACTION100
4.23-27.410.10071440.09172828X-RAY DIFFRACTION96.43

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