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- PDB-4mye: Cymosema roseum seed lectin structure complexed with X-man -

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Basic information

Entry
Database: PDB / ID: 4mye
TitleCymosema roseum seed lectin structure complexed with X-man
ComponentsCymbosema roseum mannose-specific lectin
KeywordsCarbohydrate-binding protein / Jelly roll / Lectin
Function / homology
Function and homology information


mannose binding / carbohydrate 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
: / Chem-XMM / Cymbosema roseum mannose-specific lectin / Mannose-specific lectin alpha chain
Similarity search - Component
Biological speciesCymbosema roseum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsBarroso-Neto, I.L. / Rocha, B.A.M. / Teixeira, C.S. / Santiago, M.Q. / Souza, L.A.G. / Pires, A.F. / Assreuy, A.M.S. / Delatorre, P. / Cavada, B.S.
CitationJournal: To be Published
Title: Cymosema roseum seed lectin structure complexed with X-man
Authors: Barroso-Neto, I.L. / Rocha, B.A.M. / Teixeira, C.S. / Santiago, M.Q. / Souza, L.A.G. / Pires, A.F. / Assreuy, A.M.S. / Delatorre, P. / Cavada, B.S.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 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: Cymbosema roseum mannose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8375
Polymers25,3101
Non-polymers5274
Water4,720262
1
A: Cymbosema roseum mannose-specific lectin
hetero molecules

A: Cymbosema roseum mannose-specific lectin
hetero molecules

A: Cymbosema roseum mannose-specific lectin
hetero molecules

A: Cymbosema roseum mannose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,34620
Polymers101,2404
Non-polymers2,10716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11260 Å2
ΔGint-182 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.365, 88.753, 90.626
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-520-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cymbosema roseum mannose-specific lectin


Mass: 25309.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cymbosema roseum (plant) / References: UniProt: D5MNX4, UniProt: P86184*PLUS
#4: Sugar ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6

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Non-polymers , 4 types, 265 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES sodium, pH 7.5, 20% v/v 2-Propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2012
RadiationMonochromator: Double Flat Crystal Monochromator with Fixed-exit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 59772 / Num. obs: 35883 / % possible obs: 98.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 22.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.58-1.614.20.207189.7
1.61-1.644.50.19199.9
1.64-1.674.50.162199.9
1.67-1.74.50.1471100
1.7-1.744.50.12199.9
1.74-1.784.60.107199.9
1.78-1.824.60.0911100
1.82-1.874.60.078199.9
1.87-1.934.60.0651100
1.93-1.994.60.0541100
1.99-2.064.50.0471100
2.06-2.144.50.0441100
2.14-2.244.50.0431100
2.24-2.364.50.047199.8
2.36-2.514.40.05199.7
2.51-2.74.30.047199.4
2.7-2.974.50.037199.1
2.97-3.44.70.028198.2
3.4-4.294.70.025196.5
4.29-504.40.028186.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.65 Å26.32 Å
Translation1.65 Å26.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→26.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.0979 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20854 1604 5.1 %RANDOM
Rwork0.18781 ---
obs0.18888 30066 98.7 %-
all-59772 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.454 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å2-0 Å20 Å2
2---0.48 Å2-0 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 26 262 2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021856
X-RAY DIFFRACTIONr_bond_other_d00.021687
X-RAY DIFFRACTIONr_angle_refined_deg2.2721.962540
X-RAY DIFFRACTIONr_angle_other_deg3.88733902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.755238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37224.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09715280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.162156
X-RAY DIFFRACTIONr_chiral_restr0.1510.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212107
X-RAY DIFFRACTIONr_gen_planes_other0.0280.02411
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 130 -
Rwork0.253 2219 -
obs--99.96 %

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