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- PDB-3ojb: Crystal structure of C-terminal domain of human galectin-8 -

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Basic information

Entry
Database: PDB / ID: 3ojb
TitleCrystal structure of C-terminal domain of human galectin-8
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / Jelly-roll / Carbohydrate/Sugar Binding
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 / cytoplasm / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsZhou, D. / Teng, M. / Niu, L.
CitationJournal: To be Published
Title: Crystal structure of C-terminal carbohydrate recognition domain of human galectin-8
Authors: Zhou, D. / Teng, M. / Niu, L.
History
DepositionAug 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Galectin-8
D: Galectin-8


Theoretical massNumber of molelcules
Total (without water)63,6854
Polymers63,6854
Non-polymers00
Water34219
1
A: Galectin-8


Theoretical massNumber of molelcules
Total (without water)15,9211
Polymers15,9211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-8


Theoretical massNumber of molelcules
Total (without water)15,9211
Polymers15,9211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-8


Theoretical massNumber of molelcules
Total (without water)15,9211
Polymers15,9211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-8


Theoretical massNumber of molelcules
Total (without water)15,9211
Polymers15,9211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.105, 73.148, 179.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

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


Mass: 15921.230 Da / Num. of mol.: 4 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00214
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 27.5% PEG 8000, 0.2M ammonium phosphate, 6.5% Ethylene Glycol, 0.1M Na Cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.006→50 Å / Num. all: 14838 / Num. obs: 13191 / % possible obs: 88.9 % / Redundancy: 5.49 % / Rmerge(I) obs: 0.219
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.413 / Num. unique all: 1432 / % possible all: 67.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0104refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YV8

2yv8


Resolution: 3.01→20 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.813 / SU B: 48.173 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 666 5.1 %RANDOM
Rwork0.22814 ---
obs0.23129 12427 88.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.865 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20 Å2
2--0.71 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 3.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 0 19 4211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224284
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9545780
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60923.654208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94215756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.451532
X-RAY DIFFRACTIONr_chiral_restr0.0760.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213252
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.0681.52608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.13124216
X-RAY DIFFRACTIONr_scbond_it0.27331676
X-RAY DIFFRACTIONr_scangle_it0.4144.51564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1048 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.380.5
Bmedium positional0.410.5
Cmedium positional0.340.5
Dmedium positional0.350.5
Amedium thermal0.162
Bmedium thermal0.142
Cmedium thermal0.122
Dmedium thermal0.132
LS refinement shellResolution: 3.006→3.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 38 -
Rwork0.379 641 -
obs--66.11 %
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)
11.6462-0.5087-0.06781.18620.18994.3737-0.1315-0.03670.13790.07340.09570.0325-0.10.02030.03580.07820.001-0.00750.3144-0.00860.14959.102831.106714.9782
22.38890.43930.04072.04120.28733.2888-0.06230.0336-0.08670.15410.04010.14770.0202-0.07060.02230.1166-0.00060.00330.30950.00420.146635.370326.324925.8666
33.69230.0417-0.8115.03830.04663.727-0.0703-0.1531-0.41840.0807-0.08060.12610.43650.0410.15090.2251-0.01770.03280.3641-0.03880.212715.207116.543153.0287
42.0017-0.5163-0.13244.8990.26113.6936-0.0842-0.1239-0.41570.20890.072-0.04620.4915-0.10490.01220.1951-0.02070.05220.3580.00710.316816.0598-0.926113.5722
50.08350.04380.0640.15240.14490.1635-0.0363-0.0546-0.02580.2428-0.02050.09140.19930.04430.05670.49730.05040.20960.25860.05160.093917.71323.458923.1921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 139
2X-RAY DIFFRACTION2B9 - 139
3X-RAY DIFFRACTION3C9 - 139
4X-RAY DIFFRACTION4D9 - 139
5X-RAY DIFFRACTION5A - D140 - 143

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