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- PDB-6usc: Structure of Human Intelectin-1 in complex with KO -

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Basic information

Entry
Database: PDB / ID: 6usc
TitleStructure of Human Intelectin-1 in complex with KO
ComponentsIntelectin-1
KeywordsSUGAR BINDING PROTEIN / KO / lectin / microbial recognition
Function / homology
Function and homology information


oligosaccharide binding / response to nematode / Antimicrobial peptides / protein homotrimerization / side of membrane / positive regulation of glucose import / brush border membrane / receptor complex / positive regulation of protein phosphorylation / membrane raft ...oligosaccharide binding / response to nematode / Antimicrobial peptides / protein homotrimerization / side of membrane / positive regulation of glucose import / brush border membrane / receptor complex / positive regulation of protein phosphorylation / membrane raft / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
Chem-KO2 / Intelectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsWindsor, I.W. / Isabella, C.R. / Kosma, P. / Raines, R.T. / Kiessling, L.L.
Funding support United States, Austria, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI055258 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U01 CA2310789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM044783 United States
Austrian Science FundP28826-N28 Austria
National Science Foundation (NSF, United States)1122374 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Stereoelectronic Effects Impact Glycan Recognition.
Authors: McMahon, C.M. / Isabella, C.R. / Windsor, I.W. / Kosma, P. / Raines, R.T. / Kiessling, L.L.
History
DepositionOct 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intelectin-1
B: Intelectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,98711
Polymers62,1222
Non-polymers8649
Water5,873326
1
A: Intelectin-1
hetero molecules

A: Intelectin-1
hetero molecules

A: Intelectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,53318
Polymers93,1843
Non-polymers1,35015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5700 Å2
ΔGint-148 kcal/mol
Surface area27970 Å2
MethodPISA
2
B: Intelectin-1
hetero molecules

B: Intelectin-1
hetero molecules

B: Intelectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,42715
Polymers93,1843
Non-polymers1,24312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area5380 Å2
ΔGint-125 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.145, 118.145, 118.145
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

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Components

#1: Protein Intelectin-1 / ITLN-1 / Endothelial lectin HL-1 / Galactofuranose-binding lectin / Intestinal lactoferrin receptor / Omentin


Mass: 31061.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITLN1, INTL, ITLN, LFR, UNQ640/PRO1270 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8WWA0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-KO2 / prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulopyranosidonic acid / prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulosidonic acid / prop-2-en-1-yl D-glycero-D-talo-oct-2-ulosidonic acid / prop-2-en-1-yl D-glycero-talo-oct-2-ulosidonic acid


Type: D-saccharide, alpha linking / Mass: 294.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H18O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM bis-Tris, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.59→48.24 Å / Num. obs: 73205 / % possible obs: 99.2 % / Redundancy: 35.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.023 / Rrim(I) all: 0.142 / Net I/σ(I): 16.9
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.893 / Num. unique obs: 4888 / CC1/2: 0.488 / Rpim(I) all: 0.273 / Rrim(I) all: 0.938 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
Aimless0.7.1data scaling
PDB_EXTRACTdata extraction
DIALS1.9.2data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wmq

4wmq


Resolution: 1.59→48.23 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 16.6
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 3522 4.81 %Random
Rwork0.1583 ---
obs0.1594 73170 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.83 Å2 / Biso mean: 21.93 Å2 / Biso min: 10.7 Å2
Refinement stepCycle: final / Resolution: 1.59→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 47 326 4753
Biso mean--29.38 28.9 -
Num. residues----558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Rfactor Rfree error
1.59-1.610.30941240.2754244989
1.61-1.630.30191360.2656260693
1.63-1.650.31631480.2473267797
1.65-1.680.27331220.23412789100
1.68-1.710.20641470.20122808100
1.71-1.740.21891530.19022759100
1.742-1.77370.21111200.175928061000
1.77-1.80.21781510.17282766100
1.8-1.840.21041170.17432829100
1.84-1.880.19041800.16752717100
1.88-1.920.1961300.1582855100
1.92-1.970.17591270.15382777100
1.97-2.030.19381650.14622805100
2.03-2.090.17981480.14092760100
2.09-2.150.19771310.14712824100
2.15-2.230.18231410.14972801100
2.23-2.320.19611350.15042827100
2.32-2.420.18151310.15472824100
2.42-2.550.19621440.16322793100
2.55-2.710.18541590.15982792100
2.71-2.920.19881590.165428411000
2.92-3.220.19231500.16232831100
3.22-3.680.15991090.1472874100
3.68-4.640.1311370.12622876100
4.64-48.230.14771580.15342962100

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