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- PDB-5cbl: Crystal structure of the C-terminal domain of human galectin-4 wi... -

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Basic information

Entry
Database: PDB / ID: 5cbl
TitleCrystal structure of the C-terminal domain of human galectin-4 with lactose
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / galectins / beta-galactosides binding
Function / homology
Function and homology information


antibacterial peptide biosynthetic process / galactoside binding / carbohydrate binding / collagen-containing extracellular matrix / cell adhesion / extracellular space / plasma membrane / 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
beta-lactose / BETA-MERCAPTOETHANOL / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.781 Å
AuthorsRustiguel, J.K. / Nonato, M.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/21811-1 and 2010/16153-2 Brazil
CitationJournal: Protein Expr.Purif. / Year: 2015
Title: Recombinant expression, purification and preliminary biophysical and structural studies of C-terminal carbohydrate recognition domain from human galectin-4.
Authors: Rustiguel, J.K. / Kumagai, P.S. / Dias-Baruffi, M. / Costa-Filho, A.J. / Nonato, M.C.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Data collection / Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2May 1, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-4
B: Galectin-4
C: Galectin-4
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,23012
Polymers65,5024
Non-polymers1,7288
Water5,350297
1
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7182
Polymers16,3761
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9845
Polymers16,3761
Non-polymers6094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8103
Polymers16,3761
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7182
Polymers16,3761
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.512, 126.741, 45.530
Angle α, β, γ (deg.)90.000, 99.650, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYchain AAA184 - 3239 - 148
2GLYGLYchain BBB184 - 3239 - 148
3PROPROchain CCC185 - 32310 - 148
4PROPROchain DDD186 - 32311 - 148

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Galectin-4 / Gal-4 / Antigen NY-CO-27 / L-36 lactose-binding protein / L36LBP / Lactose-binding lectin 4


Mass: 16375.621 Da / Num. of mol.: 4 / Fragment: UNP residues 179-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS4 / Plasmid: pET-28a-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P56470
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 301 molecules

#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.98 Å3/Da / Density % sol: 37.99 % / Description: twinning crystals
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 25% a 35% PEG 4000-10000, 0.2 to 0.4 M lithium or ammonium sulfate
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Number: 274222 / Rsym value: 0.101 / D res high: 1.781 Å / D res low: 63.37 Å / Num. obs: 46238 / % possible obs: 95.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
5.6363.3710.0510.0516.2
3.985.6310.0680.0686.1
3.253.9810.0750.0756.4
2.823.2510.0990.0995.8
2.522.8210.1320.1326.1
2.32.5210.1660.1665.7
2.132.310.2130.2135.9
1.992.1310.270.276
1.881.9910.3670.3675.8
1.781.8810.5060.5065.9
Reflection twinOperator: l,-k,h / Fraction: 0.27
ReflectionResolution: 1.781→63.37 Å / Num. obs: 46238 / % possible obs: 95.4 % / Redundancy: 5.9 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.111 / Rsym value: 0.101 / Net I/av σ(I): 4.5 / Net I/σ(I): 9.1 / Num. measured all: 274222
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.78-1.885.90.5063.24034668770.2260.5063.297.4
1.88-1.995.80.36723637662690.1650.3674.493.9
1.99-2.1360.272.63532158920.1180.27694.3
2.13-2.35.90.2133.23370457160.0940.2137.597.3
2.3-2.525.70.16642824049650.0740.1668.992
2.52-2.826.10.13252893747740.0570.13211.198.1
2.82-3.255.80.0996.12333540280.0440.09913.793.2
3.25-3.986.40.0758.12261535600.0310.07517.798.4
3.98-5.636.10.0688.11599626410.0290.06818.693.1
5.63-63.376.20.05110.3935215160.0210.05117.597

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.78 Å63.37 Å
Translation1.78 Å63.37 Å

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Processing

Software
NameVersionClassification
MOSFLM7.1.3data reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJB

3ojb


Resolution: 1.781→63.37 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.7 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 2075 4.49 %random selection
Rwork0.182 44162 --
obs0.1854 46206 95.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.21 Å2 / Biso mean: 29.8378 Å2 / Biso min: 9.8 Å2
Refinement stepCycle: final / Resolution: 1.781→63.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 220 297 4647
Biso mean--35.27 29.02 -
Num. residues----542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044384
X-RAY DIFFRACTIONf_angle_d0.9795966
X-RAY DIFFRACTIONf_chiral_restr0.037672
X-RAY DIFFRACTIONf_plane_restr0.004767
X-RAY DIFFRACTIONf_dihedral_angle_d11.951515
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3034X-RAY DIFFRACTION11.598TORSIONAL
12B3034X-RAY DIFFRACTION11.598TORSIONAL
13C3034X-RAY DIFFRACTION11.598TORSIONAL
14D3034X-RAY DIFFRACTION11.598TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7813-1.82580.29071520.25273254340693
1.8258-1.87520.24871430.25383159330293
1.8752-1.93040.26221470.24123160330792
1.9304-1.99260.25461360.23443040317688
1.9926-2.06380.24771320.22653053318588
2.0638-2.14640.25781410.2183181332293
2.1464-2.24410.23111470.21753271341894
2.2441-2.36230.24441470.20793145329291
2.3623-2.51020.23441390.20482954309386
2.5102-2.70380.26031510.19823281343294
2.7038-2.97550.2421440.18253182332693
2.9755-3.40530.18521340.15863075320989
3.4053-4.28710.18091490.14093252340193
4.2871-25.88830.2271430.1583155329890

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