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- PDB-7p1m: Galectin-8 N-terminal carbohydrate recognition domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 7p1m
TitleGalectin-8 N-terminal carbohydrate recognition domain in complex with benzimidazole D-galactal ligand
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / Inhibitor / complex / Galectin / Lectin / D-galactal
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane ...lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-4IU / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsHassan, M. / Hakansson, M. / Nilsson, J.U. / Kovacic, R.
Funding support Sweden, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581 Sweden
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Structure-Guided Design of d-Galactal Derivatives with High Affinity and Selectivity for the Galectin-8 N-Terminal Domain.
Authors: Hassan, M. / Baussiere, F. / Guzelj, S. / Sundin, A.P. / Hakansson, M. / Kovacic, R. / Leffler, H. / Tomasic, T. / Anderluh, M. / Jakopin, Z. / Nilsson, U.J.
History
DepositionJul 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-8
B: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8675
Polymers34,1632
Non-polymers7043
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-12 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.360, 61.820, 84.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A14 - 160
2010B14 - 160

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Components

#1: Protein Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 17081.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Chemical ChemComp-4IU / 2-[[(2R,3R,4R)-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2H-pyran-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid


Mass: 334.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 293.5 K / Method: liquid diffusion / pH: 8
Details: Buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 ...Details: Buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).

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Data collection

DiffractionMean temperature: 293.5 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.52→49.91 Å / Num. obs: 3108 / % possible obs: 99.94 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.1
Reflection shellResolution: 1.52→1.56 Å / Rmerge(I) obs: 1.61 / Num. unique obs: 0

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZD

5gzd


Resolution: 1.52→49.91 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.574 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20737 2175 4.9 %RANDOM
Rwork0.14528 ---
obs0.14837 42412 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.956 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2--5.07 Å2-0 Å2
3----3.76 Å2
Refinement stepCycle: 1 / Resolution: 1.52→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 49 283 2718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132599
X-RAY DIFFRACTIONr_bond_other_d0.0050.0172420
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.6723532
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5975626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52121.831142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28615445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6151519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022921
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5742.1061239
X-RAY DIFFRACTIONr_mcbond_other3.5732.1061240
X-RAY DIFFRACTIONr_mcangle_it4.4273.1661560
X-RAY DIFFRACTIONr_mcangle_other4.4283.1671560
X-RAY DIFFRACTIONr_scbond_it4.2712.4861360
X-RAY DIFFRACTIONr_scbond_other4.2712.4861360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0863.5841969
X-RAY DIFFRACTIONr_long_range_B_refined5.86725.6132802
X-RAY DIFFRACTIONr_long_range_B_other5.68924.9982735
X-RAY DIFFRACTIONr_rigid_bond_restr4.30535019
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4590 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 163 -
Rwork0.319 3108 -
obs--99.97 %
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)
11.6224-0.1684-0.33121.82250.0610.87980.04760.03370.05240.2065-0.1048-0.03840.0769-0.04540.05720.0953-0.034-0.02670.01430.00790.101215.342-0.082-1.5883
21.29020.2126-0.75161.3067-0.10641.5585-0.04350.14070.0352-0.22940.01720.05450.0985-0.05680.02630.08560.0055-0.00350.01790.01150.080241.482.0748-20.9326
31.02930.2644-0.54630.4862-0.0480.80910.02040.07520.0107-0.0284-0.0182-0.01050.0943-0.0374-0.00220.08190.0067-0.03750.00910.00390.102628.5919-0.5621-10.8886
400000000000000-00.1128-0.0169-0.04150.01180.05120.231931.389-5.534-7.316
500000000000000-00.0974000.097400.0974000
600000000000000-00.0974000.097400.0974000
700000000000000-00.0974000.097400.0974000
800000000000000-00.0974000.097400.0974000
92.4276-0.93553.44012.3842-2.90166.18570.0693-0.2674-0.11150.24130.06740.06140.0067-0.328-0.13670.2403-0.01840.04140.07950.00940.1159.6509-4.64388.3219
101.3416-0.57060.20020.5385-0.17441.39980.01320.15420.0316-0.0957-0.0011-0.00510.1421-0.1457-0.01220.1434-0.0137-0.0030.0925-0.01160.093338.7287-7.8793-27.7157
1100000000000000-00.0974000.097400.0974000
1200000000000000-00.0974000.097400.0974000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 156
2X-RAY DIFFRACTION2B6 - 154
3X-RAY DIFFRACTION3A301 - 436
4X-RAY DIFFRACTION4A201
5X-RAY DIFFRACTION5A7 - 156
6X-RAY DIFFRACTION6B6 - 154
7X-RAY DIFFRACTION7A301 - 436
8X-RAY DIFFRACTION8A201
9X-RAY DIFFRACTION9A14 - 156
10X-RAY DIFFRACTION10B13 - 154
11X-RAY DIFFRACTION11A301 - 436
12X-RAY DIFFRACTION12A201

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