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- PDB-1mvq: Cratylia mollis lectin (isoform 1) in complex with methyl-alpha-D... -

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Basic information

Entry
Database: PDB / ID: 1mvq
TitleCratylia mollis lectin (isoform 1) in complex with methyl-alpha-D-mannose
Componentslectin, isoform 1
KeywordsSUGAR BINDING PROTEIN / legume lectin
Function / homology
Function and homology information


glucose binding / mannose binding / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / : / Mannose/glucose-specific lectin Cramoll
Similarity search - Component
Biological speciesCratylia mollis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
Authorsde Souza, G.A. / Oliveira, P.S. / Trapani, S. / Correia, M.T. / Oliva, G. / Coelho, L.C. / Greene, L.J.
CitationJournal: Glycobiology / Year: 2003
Title: Amino acid sequence and tertiary structure of Cratylia mollis seed lectin
Authors: De Souza, G.A. / Oliveira, P.S. / Trapani, S. / Santos, A.C. / Rosa, J.C. / Laure, H.J. / Correia, M.T. / Tavares, G.A. / Oliva, G. / Coelho, L.C. / Greene, L.J.
History
DepositionSep 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _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_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: lectin, isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6834
Polymers25,3941
Non-polymers2893
Water3,225179
1
A: lectin, isoform 1
hetero molecules

A: lectin, isoform 1
hetero molecules

A: lectin, isoform 1
hetero molecules

A: lectin, isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,73316
Polymers101,5764
Non-polymers1,15712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area11030 Å2
ΔGint-109 kcal/mol
Surface area32200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.449, 77.956, 105.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

21A-392-

HOH

DetailsThe biological assembly is a tetramer - a dimer of a dimer - generated from the monomer in the asymmetric unit. The first dimer is generated by the operations: x, y, z and -x, y, -z+1. The second dimer is generated by the operations: x, -y+1, -z+1 and -x, -y+1, z

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Components

#1: Protein lectin, isoform 1 /


Mass: 25393.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Seed / Source: (natural) Cratylia mollis (plant) / References: UniProt: P83721
#2: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside / Methylglucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, microgravity / pH: 4.5
Details: PEG 6000, sodium chloride, O1-methyl-alpha-D-mannose, acetate buffer, pH 4.5, Vapor diffusion, microgravity, temperature 295K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: Tavares, G.A., (1996) Acta Crystallogr., D52, 1046.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
20.01 Msodium acetate1reservoirpH4.5
30.15 M1reservoirNaCl
49 %(w/v)PEG60001reservoir
50.01 M1reservoirNaN3
60.15 Mmethyl-alpha-D-mannopyranoside1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.77→9.94 Å / Num. all: 25553 / Num. obs: 25553 / % possible obs: 99.6 % / Redundancy: 3.76 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 0.068
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 3.72 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 1767 / Rsym value: 0.068 / % possible all: 98.1
Reflection
*PLUS
Redundancy: 3.8 % / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.345

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.09refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CNA

5cna


Resolution: 1.77→9.94 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.698 / SU ML: 0.054 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.89 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16991 1288 5 %RANDOM
Rwork0.14023 ---
all0.14173 24265 --
obs0.14173 24265 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.688 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.77→9.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 15 179 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211904
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9412610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.29815305
X-RAY DIFFRACTIONr_chiral_restr0.1230.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021399
X-RAY DIFFRACTIONr_nbd_refined0.2010.2776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.217
X-RAY DIFFRACTIONr_mcbond_it1.1041.51198
X-RAY DIFFRACTIONr_mcangle_it2.02221976
X-RAY DIFFRACTIONr_scbond_it2.8583706
X-RAY DIFFRACTIONr_scangle_it4.6334.5634
LS refinement shellResolution: 1.77→1.83 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.207 124
Rwork0.179 2256
Refinement TLS params.Method: refined / Origin x: 11.043 Å / Origin y: 24.965 Å / Origin z: 38.226 Å
111213212223313233
T0.0001 Å20.003 Å20.002 Å2-0.1496 Å2-0.0219 Å2--0.0998 Å2
L1.2375 °2-0.3185 °2-0.2831 °2-0.7974 °20.1075 °2--1.3201 °2
S-0.0345 Å °-0.0001 Å °-0.0867 Å °-0.0384 Å °0.0379 Å °-0.0059 Å °0.1401 Å °0.0714 Å °-0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2361 - 236
2X-RAY DIFFRACTION1AB2371
3X-RAY DIFFRACTION1AC - D238 - 2391
4X-RAY DIFFRACTION1AE240 - 4181 - 179
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.17 / Rfactor Rwork: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS

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