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- PDB-4z8b: crystal structure of a DGL mutant - H51G H131N -

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Basic information

Entry
Database: PDB / ID: 4z8b
Titlecrystal structure of a DGL mutant - H51G H131N
ComponentsLectin alpha chain
KeywordsSUGAR BINDING PROTEIN / Lectin / dioclea grandiflora / H31A-H151N mutant
Function / homology
Function and homology information


mannose binding / toxin activity / carbohydrate binding / identical protein 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 / Lectin alpha chain
Similarity search - Component
Biological speciesDioclea grandiflora (mucana)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsZamora-Caballero, S. / Perez, A. / Sanz, L. / Bravo, J. / Calvete, J.J.
CitationJournal: Febs Lett. / Year: 2015
Title: Quaternary structure of Dioclea grandiflora lectin assessed by equilibrium sedimentation and crystallographic analysis of recombinant mutants.
Authors: Zamora-Caballero, S. / Perez, A. / Sanz, L. / Bravo, J. / Calvete, J.J.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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 1.4Jan 10, 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

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Assembly

Deposited unit
A: Lectin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3147
Polymers25,5261
Non-polymers7886
Water1,26170
1
A: Lectin alpha chain
hetero molecules

A: Lectin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,62814
Polymers51,0522
Non-polymers1,57612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3850 Å2
ΔGint-91 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.350, 67.080, 108.620
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-462-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Lectin alpha chain


Mass: 25526.232 Da / Num. of mol.: 1 / Mutation: H51G;H131N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioclea grandiflora (mucana) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08902
#6: 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 , 5 types, 75 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: RESERVOIR SOLUTION:100 mM HEPES, 14% polyethylene glycol 400 PROTEIN SOLUTION: 10 mM HEPES, 2 mM Cl2Ca, 2 mM Cl2Mn 3 mM X-Man (5-bromo-4-chloro-3-indolyl-ALPHA-D-mannose
PH range: 7.5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.95→45.67 Å / Num. obs: 12687 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.04
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 5.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DGL

1dgl


Resolution: 1.951→45.669 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 607 4.79 %
Rwork0.2014 --
obs0.2034 12680 74.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.951→45.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 41 70 1874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031863
X-RAY DIFFRACTIONf_angle_d0.7662543
X-RAY DIFFRACTIONf_dihedral_angle_d10.918650
X-RAY DIFFRACTIONf_chiral_restr0.029289
X-RAY DIFFRACTIONf_plane_restr0.003321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9513-2.14760.2064640.20071321X-RAY DIFFRACTION33
2.1476-2.45840.31351500.2372683X-RAY DIFFRACTION68
2.4584-3.09720.32591890.26793896X-RAY DIFFRACTION97
3.0972-45.68130.2012040.16894173X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32380.41010.07950.5947-0.15711.0367-0.0346-0.12770.05780.5236-0.10090.3093-0.2945-0.580.65680.70140.1420.29190.34-0.02050.175914.035114.745623.1657
20.1964-0.31790.25741.93970.33450.8786-0.0944-0.2872-0.05121.10380.20720.0267-0.5695-0.43570.15370.75330.06940.06550.129-0.07430.13321.179911.425719.5288
31.511-0.3991-0.01311.7920.64712.77780.09770.05050.01760.41930.01990.4372-0.31-0.33950.08970.25420.0620.08910.2065-0.00490.202114.671310.76489.3719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 237 )

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