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- PDB-4nds: Crystal structure of L. decastes alpha-galactosyl-binding lectin -

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Basic information

Entry
Database: PDB / ID: 4nds
TitleCrystal structure of L. decastes alpha-galactosyl-binding lectin
ComponentsAlpha-galactosyl-binding lectin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology: / Alpha-galactosyl binding lectin / galactose binding / Alpha-galactosyl-binding lectin
Function and homology information
Biological speciesLyophyllum decastes (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.997 Å
AuthorsVan Eerde, A. / Grahn, E. / Krengel, U.
CitationJournal: Glycobiology / Year: 2015
Title: Atomic-resolution structure of the alpha-galactosyl binding Lyophyllum decastes lectin reveals a new protein family found in both fungi and plants.
Authors: van Eerde, A. / Grahn, E.M. / Winter, H.C. / Goldstein, I.J. / Krengel, U.
History
DepositionOct 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosyl-binding lectin
B: Alpha-galactosyl-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6525
Polymers20,5832
Non-polymers693
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-25 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.840, 56.774, 44.458
Angle α, β, γ (deg.)90.000, 107.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-galactosyl-binding lectin


Mass: 10291.380 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lyophyllum decastes (fungus) / Organ: fruiting bodies / References: UniProt: A7UNK4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 0.1 M HEPES sodium, 28% v/v PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 17, 2007
RadiationMonochromator: diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionNumber: 504759 / Rmerge(I) obs: 0.045 / D res high: 1.68 Å / Num. obs: 35395 / % possible obs: 95.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1.681.73179564.310.152
1.731.77227185.910.115
1.771.8224879510.104
1.821.88243499.210.09
1.881.94248510010.074
1.942.01234799.910.063
2.012.09226099.810.057
2.092.17221199.510.051
2.172.27208510010.049
2.272.38202199.710.048
2.382.51189599.710.046
2.512.66180999.910.046
2.662.84167410010.044
2.843.07156299.910.044
3.073.36147499.910.042
3.363.76130999.510.038
3.764.34117199.610.035
4.345.3296310010.033
5.327.5275299.510.036
7.5217.2883909410.033
ReflectionResolution: 0.997→20 Å / Num. all: 84161 / Num. obs: 84151 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14
Reflection shellResolution: 0.997→1.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.7 / % possible all: 92

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
RESOLVEphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 0.997→17.288 Å / Occupancy max: 1 / Occupancy min: 0.08 / SU ML: 0.07 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 10.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1245 4235 5.03 %RANDOM
Rwork0.1091 ---
all0.11 84151 --
obs0.1099 84142 93.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.45 Å2 / Biso mean: 11.3947 Å2 / Biso min: 3.12 Å2
Refinement stepCycle: LAST / Resolution: 0.997→17.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 3 306 1753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081684
X-RAY DIFFRACTIONf_angle_d1.3452309
X-RAY DIFFRACTIONf_chiral_restr0.081232
X-RAY DIFFRACTIONf_plane_restr0.008315
X-RAY DIFFRACTIONf_dihedral_angle_d11.503627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.997-1.00810.2157850.19371433151851
1.0081-1.01990.22461380.20212595273392
1.0199-1.03240.21051410.18372672281393
1.0324-1.04540.21211390.16942625276493
1.0454-1.05920.15831420.1592685282793
1.0592-1.07370.17891380.14542631276994
1.0737-1.0890.15521480.13522688283693
1.089-1.10530.13861370.1252652278995
1.1053-1.12260.12581400.11682695283594
1.1226-1.1410.12361440.1122711285596
1.141-1.16060.12081410.10132688282994
1.1606-1.18170.11461480.12728287697
1.1817-1.20440.13721450.09322734287995
1.2044-1.2290.11351430.09242748289197
1.229-1.25570.12511470.0932750289796
1.2557-1.28490.10011460.09042768291497
1.2849-1.31710.09881460.09162745289197
1.3171-1.35270.12251470.08682787293497
1.3527-1.39240.10331460.08452772291898
1.3924-1.43740.10461450.08382783292898
1.4374-1.48870.09561500.07662824297498
1.4887-1.54830.09121370.07562794293198
1.5483-1.61870.09291430.07862811295499
1.6187-1.7040.10681330.08372851298499
1.704-1.81060.1091410.08692837297899
1.8106-1.95030.10821620.09492848301099
1.9503-2.14620.09911570.09242815297299
2.1462-2.4560.11931460.10122833297998
2.456-3.09140.13541490.12972686283594
3.0914-17.29020.17681110.19121718182959

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