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- PDB-4akb: Structure of Galactose Binding lectin from Champedak (CGB) with G... -

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Basic information

Entry
Database: PDB / ID: 4akb
TitleStructure of Galactose Binding lectin from Champedak (CGB) with Galactose
Components
  • AGGLUTININ ALPHA CHAIN
  • AGGLUTININ BETA-4 CHAIN
KeywordsSUGAR BINDING PROTEIN / LECTIN
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Agglutinin alpha chain / Agglutinin beta-4 chain
Similarity search - Component
Biological speciesARTOCARPUS INTEGER (campedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGabrielsen, M. / Abdul-Rahman, P.S. / Othman, S. / Hashim, O.H. / Cogdell, R.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structures and Binding Specificity of Galactose- and Mannose-Binding Lectins from Champedak: Differences from Jackfruit Lectins
Authors: Gabrielsen, M. / Abdul-Rahman, P.S. / Othman, S. / Hashim, O.H. / Cogdell, R.J.
History
DepositionFeb 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA-4 CHAIN
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA-4 CHAIN
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA-4 CHAIN
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA-4 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,10612
Polymers67,2838
Non-polymers8234
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-67.1 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.286, 121.030, 77.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
AGGLUTININ ALPHA CHAIN / JACALIN ALPHA CHAIN / CHAMPEDAK GALACTOSE BINDING LECTIN ALPHA CHAIN


Mass: 14662.517 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ARTOCARPUS INTEGER (campedak) / References: UniProt: P18670
#2: Protein/peptide
AGGLUTININ BETA-4 CHAIN / CHAMPEDAK GALACTOSE BINDING LECTIN BETA CHAIN


Mass: 2158.325 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ARTOCARPUS INTEGER (campedak) / References: UniProt: Q9S8T0
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCROSS-REFERENCE IS TO NEAREST UNIPROT BUT SEQUENCE IS VARIANT WITH GENBANK REFERENCE GB FR728240.

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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: 2.65 Å3/Da / Density % sol: 53.7 % / Description: NONE
Crystal growpH: 7.6
Details: 40% PEG 600, 100 MM PHOSPHATE/CITRATE BUFFER PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→77.61 Å / Num. obs: 52244 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 10.3 % / Biso Wilson estimate: 28.88 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AK4
Resolution: 1.95→28.55 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9272 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.119
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 2628 5.04 %RANDOM
Rwork0.1713 ---
obs0.1725 52163 98.21 %-
Displacement parametersBiso mean: 35.92 Å2
Baniso -1Baniso -2Baniso -3
1-4.9904 Å20 Å20 Å2
2---9.2458 Å20 Å2
3---4.2554 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 45 266 4905
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014779HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066484HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1551SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes694HARMONIC5
X-RAY DIFFRACTIONt_it4779HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion16.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion617SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5663SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2327 186 5.12 %
Rwork0.2112 3450 -
all0.2123 3636 -
obs--98.21 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.26220.11610.16833.3187-1.03291.40680.0051-0.01090.0669-0.0971-0.2601-0.6842-0.02680.18030.255-0.13630.01260.0422-0.12230.07080.085319.582849.425415.8406
20.32161.96381.07781.01480.45180.4178-0.0199-0.07970.06550.0451-0.0964-0.0592-0.08290.00540.1163-0.0063-0.0018-0.0303-0.02170.00050.02596.869347.017922.9797
32.48250.8193-0.23742.24560.18930.8027-0.14150.47760.2873-0.43350.11480.3306-0.0601-0.12480.0267-0.01910.0093-0.1082-0.08310.0497-0.0569-14.223345.8190.5118
40.86941.0255-0.57220.24280.024900.00560.2476-0.123-0.31930.0236-0.01610.1696-0.1083-0.02930.08130.0161-0.025-0.0379-0.028-0.0439-3.026134.78053.212
51.8834-0.23860.67880.444-0.05010.88110.0373-0.1575-0.12890.0176-0.0211-0.03390.10890.0377-0.0162-0.0733-0.0028-0.014-0.00120.0650.004712.420529.933634.9097
61.3601-2.3024-0.4740.5474-0.849500.03360.2035-0.1723-0.1-0.17570.05540.01520.18940.1421-0.02380.0125-0.0228-0.02830.02570.03829.766529.360218.6402
72.74960.68551.20351.02820.36362.12080.2447-0.1461-0.46070.0554-0.0846-0.0670.3121-0.2939-0.1601-0.0325-0.0491-0.0838-0.11750.0131-0.0043-17.208621.31314.3365
80.3821-0.1445-0.28620-0.07330.6107-0.0384-0.08880.0129-0.1265-0.05890.095-0.0994-0.03660.0973-0.0167-0.0021-0.0279-0.0021-0.02150.0141-12.659235.619620.0803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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