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- PDB-9vbw: Lectin FRIL from Lablab purpureus complexed to Lewis X tetrasaccharide -

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Basic information

Entry
Database: PDB / ID: 9vbw
TitleLectin FRIL from Lablab purpureus complexed to Lewis X tetrasaccharide
ComponentsFlt3 receptor-interacting lectin
KeywordsPLANT PROTEIN / Flt3 receptor-interacting lectin / carbohydrate binding protein / lectin / glycoprotein / complex type glycan / FRIL
Function / homology
Function and homology information


protein storage vacuole lumen / carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / : / Legume lectin, beta chain, Mn/Ca-binding site / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / Flt3 receptor-interacting lectin
Similarity search - Component
Biological speciesLablab purpureus (hyacinth bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsNguyen, V.H.T. / Chen, T.H. / Chen, X. / Liu, Y.M. / Ma, C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IA-113-L02 Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-001-034-MY3 Taiwan
CitationJournal: Nat Commun / Year: 2026
Title: Altering the carbohydrate-binding specificity of the legume lectin FRIL through structure-guided engineering
Authors: Liu, Y.M. / Nguyen, H.T.V. / Chen, X. / Shahed-Al-Mahmud, M. / Chen, T.H. / Liao, K.S. / Lo, J.M. / Kan, T.C. / Ren, C.T. / Ma, C.
History
DepositionJun 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flt3 receptor-interacting lectin
E: Flt3 receptor-interacting lectin
C: Flt3 receptor-interacting lectin
G: Flt3 receptor-interacting lectin
I: Flt3 receptor-interacting lectin
M: Flt3 receptor-interacting lectin
H: Flt3 receptor-interacting lectin
D: Flt3 receptor-interacting lectin
J: Flt3 receptor-interacting lectin
P: Flt3 receptor-interacting lectin
L: Flt3 receptor-interacting lectin
O: Flt3 receptor-interacting lectin
B: Flt3 receptor-interacting lectin
F: Flt3 receptor-interacting lectin
N: Flt3 receptor-interacting lectin
K: Flt3 receptor-interacting lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,78764
Polymers465,20116
Non-polymers12,58648
Water15,457858
1
A: Flt3 receptor-interacting lectin
C: Flt3 receptor-interacting lectin
D: Flt3 receptor-interacting lectin
B: Flt3 receptor-interacting lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,44716
Polymers116,3004
Non-polymers3,14712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-42 kcal/mol
Surface area32040 Å2
MethodPISA
2
E: Flt3 receptor-interacting lectin
G: Flt3 receptor-interacting lectin
H: Flt3 receptor-interacting lectin
F: Flt3 receptor-interacting lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,44716
Polymers116,3004
Non-polymers3,14712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-44 kcal/mol
Surface area32050 Å2
MethodPISA
3
I: Flt3 receptor-interacting lectin
L: Flt3 receptor-interacting lectin
hetero molecules

J: Flt3 receptor-interacting lectin
K: Flt3 receptor-interacting lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,44716
Polymers116,3004
Non-polymers3,14712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area13840 Å2
ΔGint-41 kcal/mol
Surface area32090 Å2
MethodPISA
4
O: Flt3 receptor-interacting lectin
N: Flt3 receptor-interacting lectin
hetero molecules

M: Flt3 receptor-interacting lectin
hetero molecules

P: Flt3 receptor-interacting lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,44716
Polymers116,3004
Non-polymers3,14712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
crystal symmetry operation1_545x,y-1,z1
Buried area13900 Å2
ΔGint-43 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.825, 75.237, 241.808
Angle α, β, γ (deg.)90.00, 95.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Flt3 receptor-interacting lectin


Mass: 29075.068 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Lablab purpureus (hyacinth bean) / References: UniProt: Q9ZTA9
#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 16 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-4/a2-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.2 M ammonium fluoride, pH 6.2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→29.14 Å / Num. obs: 128114 / % possible obs: 83.5 % / Redundancy: 2.8 % / CC1/2: 0.961 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.3
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.402 / Num. unique obs: 11275 / CC1/2: 0.805 / % possible all: 74.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
SCALAdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QMO

1qmo


Resolution: 2.49→29.14 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1997 1.56 %
Rwork0.2066 --
obs0.2072 128038 83.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29077 0 784 858 30719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00530698
X-RAY DIFFRACTIONf_angle_d0.92842086
X-RAY DIFFRACTIONf_dihedral_angle_d9.29517906
X-RAY DIFFRACTIONf_chiral_restr0.0614947
X-RAY DIFFRACTIONf_plane_restr0.0055239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.55120.30881200.27047607X-RAY DIFFRACTION71
2.5512-2.62010.33241370.26248611X-RAY DIFFRACTION80
2.6201-2.69720.30141430.24919014X-RAY DIFFRACTION84
2.6972-2.78420.29871470.2539274X-RAY DIFFRACTION87
2.7842-2.88360.30191470.25399310X-RAY DIFFRACTION87
2.8836-2.99890.30241470.24939236X-RAY DIFFRACTION86
2.9989-3.13530.29451450.24599115X-RAY DIFFRACTION85
3.1353-3.30040.27651390.23188803X-RAY DIFFRACTION82
3.3004-3.50680.30221380.21988739X-RAY DIFFRACTION81
3.5068-3.7770.23891330.20548398X-RAY DIFFRACTION78
3.777-4.15620.24121360.19248555X-RAY DIFFRACTION79
4.1562-4.75530.18461370.1618625X-RAY DIFFRACTION80
4.7553-5.98270.20541590.16179973X-RAY DIFFRACTION92
5.9827-29.140.17491690.174410781X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -29.9832 Å / Origin y: -4.9006 Å / Origin z: -59.7072 Å
111213212223313233
T0.2425 Å2-0.0088 Å20.0081 Å2-0.2299 Å20.0222 Å2--0.2388 Å2
L0.0662 °2-0.0058 °20.0136 °2-0.0076 °20.019 °2--0.006 °2
S0.0065 Å °-0.0118 Å °0.0196 Å °0.0102 Å °-0.0038 Å °0.0025 Å °0.011 Å °-0.0073 Å °-0.0015 Å °
Refinement TLS groupSelection details: all

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