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- PDB-1qmo: Structure of FRIL, a legume lectin that delays hematopoietic prog... -

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Basic information

Entry
Database: PDB / ID: 1qmo
TitleStructure of FRIL, a legume lectin that delays hematopoietic progenitor maturation
Components(MANNOSE BINDING LECTIN, FRIL) x 2
KeywordsLECTIN / CROSSLINK / HEMATOPOIETIC PROGENITOR / SUGAR COMPLEX
Function / homology
Function and homology information


protein storage vacuole lumen / carbohydrate binding
Similarity search - Function
Immunoglobulin-like - #4220 / 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 ...Immunoglobulin-like - #4220 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / : / : / Flt3 receptor-interacting lectin
Similarity search - Component
Biological speciesDOLICHOS LAB LAB (hyacinth bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHamelryck, T.W. / Moore, J.G. / Chrispeels, M. / Loris, R. / Wyns, L.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Role of Weak Protein-Protein Interactions in Multivalent Lectin-Carbohydrate Binding: Crystal Structure of Cross-Linked Fril
Authors: Hamelryck, T.W. / Moore, J.G. / Chrispeels, M.J. / Loris, R. / Wyns, L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Cdna Cloning of Fril, a Lectin from Dolichos Lablab, that Preserves Hematopoietic Progenitors in Suspension Culture.
Authors: Colucci, G. / Moore, J.G. / Feldman, M. / Chrispeels, M.J.
#2: Journal: Glycobiology / Year: 1999
Title: Purification and Characterization of Dolichos Lablab Lectin
Authors: Mo, H. / Meah, Y. / Moore, J.G. / Goldstein, I.J.
History
DepositionOct 4, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 1999Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references / Derived calculations / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANNOSE BINDING LECTIN, FRIL
B: MANNOSE BINDING LECTIN, FRIL
C: MANNOSE BINDING LECTIN, FRIL
D: MANNOSE BINDING LECTIN, FRIL
E: MANNOSE BINDING LECTIN, FRIL
F: MANNOSE BINDING LECTIN, FRIL
G: MANNOSE BINDING LECTIN, FRIL
H: MANNOSE BINDING LECTIN, FRIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,90520
Polymers108,8048
Non-polymers1,10112
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49220 Å2
ΔGint-315.4 kcal/mol
Surface area41020 Å2
MethodPQS
Unit cell
Length a, b, c (Å)151.360, 151.360, 309.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99877, -0.00229, -0.04957), (-0.00243, -0.99999, -0.00286), (-0.04956, 0.00298, -0.99877)1.75386, 2.64928, 73.38818
2given(-1, 0.00171, -0.00027), (0.00171, 1, 0.00061), (0.00027, 0.00061, -1)151.40465, -0.12035, 69.63332
3given(-0.99882, 0.00088, 0.04847), (-0.00106, -0.99999, -0.00379), (0.04847, -0.00384, 0.99882)149.66263, 2.60639, -3.69045
DetailsTHE BIOMOLECULE CONSISTS OF A TETRAMER OF A HETERO-DIMER.THE HETERO DIMER APPEARS TO BE A RESULT OF POST-TRANSLATIONALPROCESSING OF THE SINGLE GENE PRODUCT.

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Components

#1: Protein
MANNOSE BINDING LECTIN, FRIL


Mass: 12212.475 Da / Num. of mol.: 4 / Fragment: ALPHA CHAIN RESIDUES 1 TO 113 / Source method: isolated from a natural source / Source: (natural) DOLICHOS LAB LAB (hyacinth bean) / Organ: SEED / References: GenBank: 4204466, UniProt: Q9ZTA9*PLUS
#2: Protein
MANNOSE BINDING LECTIN, FRIL


Mass: 14988.616 Da / Num. of mol.: 4 / Fragment: BETA CHAIN RESIDUES 132 TO 264 / Source method: isolated from a natural source / Source: (natural) DOLICHOS LAB LAB (hyacinth bean) / Organ: SEED / References: GenBank: 4204466, UniProt: Q9ZTA9*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsTHE HETERO-DIMER, CHAINS A,E ARE THE PRODUCT OF A SINGLE GENE AND IS LIKELY DUE TO PROTEOLYTICAL PROCESSING

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 5.12 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.5
Details: METHOD 'HANING DROP BOTTOM', 20 % PEG 8000, 0.1 M NACACODYLATE, PH 6.5, 0.2 M (NH4)2SO4, WITH A 5 MICROLITER PROTEIN SOLUTION DROP, (4.3 MG/ML)+ 5 MICROLITER BOTTOM SOLUTION + 1 MICROLITER ...Details: METHOD 'HANING DROP BOTTOM', 20 % PEG 8000, 0.1 M NACACODYLATE, PH 6.5, 0.2 M (NH4)2SO4, WITH A 5 MICROLITER PROTEIN SOLUTION DROP, (4.3 MG/ML)+ 5 MICROLITER BOTTOM SOLUTION + 1 MICROLITER TRIMANNOSIDE SOLUTION (90 MM)
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.3 mg/mlprotein1drop
290 mMMan(alpha1-3)[Man(alpha1-6)]Man(alpha1-O-Me)1drop
411 %PEG80001reservoirbottom solution
50.1 MNa cacodylate1reservoirbottom solution
60.2 Mammonium sulfate1reservoirbottom solution
3bottom solution1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 333806 / % possible obs: 99.4 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.3
Reflection shellResolution: 3.5→3.62 Å / Mean I/σ(I) obs: 4.8
Reflection
*PLUS
Num. obs: 26919 / Num. measured all: 257389 / Rmerge(I) obs: 0.159

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL

Resolution: 3.5→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: NO DENSITY FOR RESIDUES AFTER POSITION 248. GAP BETWEEN ASN 113 AND SER 132, LIKELY DUE TO PROTEOLYTICAL PROCESSING
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2681 10 %RANDOM
Rwork0.232 ---
obs0.232 26919 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.168158 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-22.3 Å20 Å2
2---1.62 Å20 Å2
3---3.241 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 56 0 7148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.53.504
X-RAY DIFFRACTIONc_mcangle_it0.75.981
X-RAY DIFFRACTIONc_scbond_it0.54.721
X-RAY DIFFRACTIONc_scangle_it0.87.418
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 449 10.2 %
Rwork0.321 3942 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAM
X-RAY DIFFRACTION3PARAM.METALS
X-RAY DIFFRACTION4CARBOHYDRATE.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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