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- PDB-7bbi: Joint X-ray/neutron room temperature structure of H/D-exchanged P... -

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Basic information

Entry
Database: PDB / ID: 7bbi
TitleJoint X-ray/neutron room temperature structure of H/D-exchanged PLL lectin
ComponentsPLL lectin
KeywordsSUGAR BINDING PROTEIN / propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / Uncharacterized protein
Function and homology information
Biological speciesPhotorhabdus laumondii (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M.
Funding support France, 1items
OrganizationGrant numberCountry
Other private France
CitationJournal: Structure / Year: 2021
Title: Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions.
Authors: Gajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLL lectin


Theoretical massNumber of molelcules
Total (without water)41,9451
Polymers41,9451
Non-polymers00
Water6,125340
1
A: PLL lectin

A: PLL lectin

A: PLL lectin

A: PLL lectin


Theoretical massNumber of molelcules
Total (without water)167,7804
Polymers167,7804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area7690 Å2
ΔGint-44 kcal/mol
Surface area45850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.680, 89.340, 159.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

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Components

#1: Protein PLL lectin


Mass: 41944.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii (bacteria) / Gene: CKY10_20885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A329WTS5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, pD 4.2, 8 % (w/v) PEG 4000 dissolved in D2O

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.98
NUCLEAR REACTORILL LADI III23.1-4.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDOct 24, 2018
LADI III2IMAGE PLATESep 3, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
23.11
34.11
Reflection

Biso Wilson estimate: 20.07 Å2 / Entry-ID: 7BBI

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.7-465657798.63.510.064112.4
2.2-392185582.92.80.1822.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID
1.7-2.020.7841570.631
2.2-2.320.4627972

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
SCALAdata scaling
PHENIXphasing
Refinement
Method to determine structureStarting modelResolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLDiffraction-IDCross valid methodσ(F)Phase errorShrinkage radii (Å)VDW probe radii (Å)Stereochemistry target valuesSolvent model
MOLECULAR REPLACEMENT5c9o

5c9o

1.7-39.84X-RAY DIFFRACTION31.760.15610.13460.135728285374056568598.630.21FREE R-VALUE1.3515.22890.91.11GeoStd + Monomer Library + CDL v1.2FLAT BULK SOLVENT MODEL
MOLECULAR REPLACEMENT5c9o

5c9o

2.2-38.97NEUTRON DIFFRACTION31.760.23960.2150.2162109221821581.510.22FREE R-VALUE15.22890.91.11GeoStd + Monomer Library + CDL v1.2FLAT BULK SOLVENT MODEL
X-RAY+NEUTRON
Refinement stepCycle: LAST / Resolution: 1.7→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 0 340 3090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY+NEUTRONf_bond_d0.01026941
X-RAY+NEUTRONf_angle_d1.311511575
X-RAY+NEUTRONf_chiral_restr0.0861447
X-RAY+NEUTRONf_plane_restr0.00651387
X-RAY+NEUTRONf_dihedral_angle_d15.6082472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.41591410.41812684X-RAY DIFFRACTION99.75
1.73-1.760.29271410.30392692X-RAY DIFFRACTION99.51
1.76-1.790.26181410.24482679X-RAY DIFFRACTION99.79
1.79-1.830.20751400.19742664X-RAY DIFFRACTION99.61
1.83-1.870.21311420.17342702X-RAY DIFFRACTION99.82
1.87-1.910.20471420.16612696X-RAY DIFFRACTION99.44
1.91-1.960.18991420.16932688X-RAY DIFFRACTION99.51
1.96-2.020.16821410.15952678X-RAY DIFFRACTION99.51
2.02-2.070.16731400.13242675X-RAY DIFFRACTION99.4
2.07-2.140.171430.13382698X-RAY DIFFRACTION99.02
2.14-2.220.15071410.12722677X-RAY DIFFRACTION99.19
2.22-2.310.13141400.1222682X-RAY DIFFRACTION99.12
2.31-2.410.16691410.12532697X-RAY DIFFRACTION98.61
2.41-2.540.1591420.13012668X-RAY DIFFRACTION98.32
2.54-2.70.14661410.1362670X-RAY DIFFRACTION98.29
2.7-2.910.17091410.13792687X-RAY DIFFRACTION97.89
2.91-3.20.171400.13012669X-RAY DIFFRACTION97.57
3.2-3.660.15211430.11662684X-RAY DIFFRACTION97.18
3.66-4.610.10361400.09592690X-RAY DIFFRACTION96.42
4.61-39.840.10931460.10472760X-RAY DIFFRACTION95.06

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