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- PDB-1zgs: Parkia platycephala seed lectin in complex with 5-bromo-4-chloro-... -

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Basic information

Entry
Database: PDB / ID: 1zgs
TitleParkia platycephala seed lectin in complex with 5-bromo-4-chloro-3-indolyl-a-D-mannose
ComponentsMannose/glucose-specific lectin
KeywordsSUGAR BINDING PROTEIN / beta prism / lectin / X-man
Function / homology
Function and homology information


glucose binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / mannose binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-XMM / Mannose/glucose-specific lectin
Similarity search - Component
Biological speciesParkia platycephala (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGallego del Sol, F. / Cavada, B.S. / Calvete, J.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The first crystal structure of a mimosoideae lectin reveals a novel quaternary arrangement of a widespread domain.
Authors: Gallego Del Sol, F. / Nagano, C. / Cavada, B.S. / Calvete, J.J.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose/glucose-specific lectin
B: Mannose/glucose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5858
Polymers95,1342
Non-polymers2,4526
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-32 kcal/mol
Surface area36520 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)80.239, 114.177, 80.304
Angle α, β, γ (deg.)90.00, 119.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mannose/glucose-specific lectin


Mass: 47566.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Parkia platycephala (plant) / Tissue: seedsSeed / References: UniProt: P83304
#2: Sugar
ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (5-BROMO-4-CHLORO-3-INDOLYL)-A-D-MANNOSE


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.3 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0M ammonium dihydrogen phosphate, 0.1M Tris-hydrochloride, 3mM, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.91995, 0.91932, 0.92191
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 23, 2004
RadiationMonochromator: sinchrotron / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.919951
20.919321
30.921911
ReflectionResolution: 2.5→69.673 Å / Num. all: 43436 / Num. obs: 43436 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.048 / Rsym value: 0.04 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6288 / Rsym value: 0.138 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.415 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24387 3929 9.1 %RANDOM
Rwork0.2085 ---
all0.2117 43403 --
obs0.2117 39474 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.301 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.88 Å2
2---0.07 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6668 0 138 203 7009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226940
X-RAY DIFFRACTIONr_angle_refined_deg3.161.9449436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84724.359273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.694151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.921510
X-RAY DIFFRACTIONr_chiral_restr0.10.21005
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025332
X-RAY DIFFRACTIONr_nbd_refined0.2090.22997
X-RAY DIFFRACTIONr_nbtor_refined0.320.24732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2356
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.25
X-RAY DIFFRACTIONr_mcbond_it1.0741.54298
X-RAY DIFFRACTIONr_mcangle_it1.91526893
X-RAY DIFFRACTIONr_scbond_it2.54132642
X-RAY DIFFRACTIONr_scangle_it3.7934.52543
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 284 -
Rwork0.266 2868 -
obs-2868 100 %

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