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- PDB-4ak4: High resolution structure of Galactose Binding lectin from Champe... -

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Basic information

Entry
Database: PDB / ID: 4ak4
TitleHigh resolution structure of Galactose Binding lectin from Champedak (CGB)
Components
  • AGGLUTININ ALPHA CHAIN
  • AGGLUTININ BETA-4 CHAIN
KeywordsSUGAR BINDING PROTEIN / LECTIN / PLANT / MANNOSE
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / 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 / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Agglutinin alpha chain / Agglutinin beta-4 chain
Similarity search - Component
Biological speciesARTOCARPUS INTEGER (chempedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGabrielsen, M. / Abdul-Rahman, P.S. / Othman, S. / Hashim, O.H. / Cogdell, R.J.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary Structural Studies of Champedak Galactose-Binding Lectin.
Authors: Gabrielsen, M. / Riboldi-Tunnicliffe, A. / Abdul-Rahman, P.S. / Mohamed, E. / Ibrahim, W.I.W. / Hashim, O.H. / Isaacs, N.W. / Cogdell, R.J.
History
DepositionFeb 21, 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
I: AGGLUTININ ALPHA CHAIN
J: AGGLUTININ BETA-4 CHAIN
K: AGGLUTININ ALPHA CHAIN
L: AGGLUTININ BETA-4 CHAIN
M: AGGLUTININ ALPHA CHAIN
N: AGGLUTININ BETA-4 CHAIN
O: AGGLUTININ ALPHA CHAIN
P: AGGLUTININ BETA-4 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,48522
Polymers134,79116
Non-polymers1,6946
Water17,511972
1
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)68,52512
Polymers67,3968
Non-polymers1,1294
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-67.5 kcal/mol
Surface area23440 Å2
MethodPISA
2
M: AGGLUTININ ALPHA CHAIN
N: AGGLUTININ BETA-4 CHAIN
O: AGGLUTININ ALPHA CHAIN
P: AGGLUTININ BETA-4 CHAIN
hetero molecules

I: AGGLUTININ ALPHA CHAIN
J: AGGLUTININ BETA-4 CHAIN
K: AGGLUTININ ALPHA CHAIN
L: AGGLUTININ BETA-4 CHAIN


Theoretical massNumber of molelcules
Total (without water)67,96010
Polymers67,3968
Non-polymers5652
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area13020 Å2
ΔGint-71.2 kcal/mol
Surface area23940 Å2
MethodPISA
3
I: AGGLUTININ ALPHA CHAIN
J: AGGLUTININ BETA-4 CHAIN
K: AGGLUTININ ALPHA CHAIN
L: AGGLUTININ BETA-4 CHAIN

M: AGGLUTININ ALPHA CHAIN
N: AGGLUTININ BETA-4 CHAIN
O: AGGLUTININ ALPHA CHAIN
P: AGGLUTININ BETA-4 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,96010
Polymers67,3968
Non-polymers5652
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area13020 Å2
ΔGint-71.2 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.171, 121.729, 77.736
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14690.569 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ARTOCARPUS INTEGER (chempedak) / References: UniProt: P18670
#2: Protein/peptide
AGGLUTININ BETA-4 CHAIN / JACALIN BETA-4 CHAIN


Mass: 2158.325 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ARTOCARPUS INTEGER (chempedak) / References: UniProt: Q9S8T0
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 2.67 Å3/Da / Density % sol: 53.99 % / Description: NONE
Crystal growDetails: 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 QUANTUM 315 / 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: 1.65→122.17 Å / Num. obs: 169730 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 22.22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.9 / % possible all: 80.2

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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 1KU8

1ku8


Resolution: 1.65→24.16 Å / Cor.coef. Fo:Fc: 0.9599 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.08
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 8207 5.02 %RANDOM
Rwork0.1648 ---
obs0.1661 163499 96.36 %-
Displacement parametersBiso mean: 26.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.359 Å20 Å20.2034 Å2
2---1.7002 Å20 Å2
3----0.6588 Å2
Refinement stepCycle: LAST / Resolution: 1.65→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9221 0 46 972 10239
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099648HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0113103HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3140SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes186HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1425HARMONIC5
X-RAY DIFFRACTIONt_it9648HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion15.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1229SEMIHARMONIC5
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_contact11402SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2581 429 4.6 %
Rwork0.2157 8888 -
all0.2176 9317 -
obs--96.36 %
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)
11.4091-0.0685-0.44510.30840.06480.35740.0609-0.10860.11180.0081-0.02120.0312-0.0666-0.0093-0.0397-0.0327-0.00110.01430.042-0.032-0.00346.959-29.161434.1675
21.0309-0.1511-0.12411.3556-0.1683-0.0028-0.00180.07680.1551-0.1351-0.0684-0.0884-0.148-0.11180.07020.0024-0.00840.02680.0239-0.01680.00618.6253-28.858717.9473
32.12450.6461-1.22090.6802-0.62071.58760.239-0.27810.31130.1117-0.1140.0493-0.25650.3025-0.125-0.0266-0.05690.038-0.0014-0.0159-0.001136.4092-21.442213.3632
40.99910.2816-0.90-0.66140.8932-0.0155-0.131-0.02050.0464-0.1127-0.0734-0.03540.11970.1282-0.0134-0.01370.02880.05810.0128-0.005632.5627-34.795418.68
50.7748-0.1425-0.02590.9580.11830.4560.0287-0.0137-0.0815-0.0158-0.04030.13510.0383-0.04280.0116-0.0131-0.0117-0.0104-0.0138-0.00290.0091-0.7169-49.212615.4379
61.34790.5473-0.46010.8319-0.2566-0.010.0229-0.1116-0.1488-0.0788-0.053-0.15350.17180.10010.0301-0.0070.00770.01330.0293-0.00810.021314.073-46.728522.0847
71.48380.51-0.19331.8941-0.42680.5924-0.11340.231-0.1596-0.41550.0091-0.27090.0910.02380.10420.0420.00620.0893-0.01720.0003-0.046232.8739-46.1352-0.2683
80.75220.6431-0.93190.52170.11030.32570.01830.07480.092-0.2137-0.00070.0281-0.0316-0.0352-0.01770.0224-0.01050.01960.01850.02360.001922.7101-35.382.4504
90.8016-0.3547-0.11451.2392-0.31510.3198-0.0903-0.1680.12830.37720.0549-0.2492-0.02760.04530.03530.11260.0068-0.1117-0.0432-0.0131-0.0412-4.8522-14.7926-0.3785
100.0981-0.92910.63460-0.440.6333-0.0173-0.061-0.11280.19510.04750.08060.1457-0.0686-0.03020.09690.002-0.0372-0.0173-0.0012-0.0197-14.9982-26.0413-2.8308
111.6471-0.18781.02830.7706-0.10721.79270.05210.2766-0.15330.0609-0.0029-0.02830.11480.363-0.0492-0.020.0283-0.01370.0256-0.0233-0.0451-1.0029-38.6008-15.1805
12-0.0126-0.50720.5810-1.12492.1058-0.02660.14760.01180.0877-0.0533-0.0278-0.12890.08840.07990.0241-0.0093-0.04070.04570.0051-0.0255-5.682-24.619-20.732
131.34770.23430.45670.23350.05120.64870.03680.0341-0.0072-0.0117-0.03310.04790.062-0.0366-0.0037-0.0388-0.0027-0.01560.03-0.03770.006545.7814-29.9183-35.8476
140.04771.03960.117800.15080.95420.0168-0.1229-0.05950.0481-0.09330.00730.1674-0.1840.07650.00520.0061-0.01690.0334-0.04870.013546.8607-30.7826-19.9922
150.8080.06530.10541.9080.73110.67060.03730.01510.07280.1499-0.26660.54590.0418-0.12260.2292-0.0738-0.0090.0433-0.0284-0.08370.097537.9844-10.7024-16.5282
160.3965-0.61380.78662.3487-0.11590.43310.03310.0930.10580.0024-0.14380.0122-0.1819-0.090.1107-0.0210.0105-0.0190.0398-0.0280.012652.4816-12.8605-23.4709
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
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L
13X-RAY DIFFRACTION13CHAIN M
14X-RAY DIFFRACTION14CHAIN N
15X-RAY DIFFRACTION15CHAIN O
16X-RAY DIFFRACTION16CHAIN P

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