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- PDB-4wmq: Structure of Human Intelectin-1 -

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Basic information

Entry
Database: PDB / ID: 4wmq
TitleStructure of Human Intelectin-1
ComponentsIntelectin-1
KeywordsSUGAR BINDING PROTEIN / lectin / disulfide-linked / carbohydrate-binding / innate immunity / calcium / microbe-binding / microbe-specific
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Recognition of microbial glycans by human intelectin-1.
Authors: Wesener, D.A. / Wangkanont, K. / McBride, R. / Song, X. / Kraft, M.B. / Hodges, H.L. / Zarling, L.C. / Splain, R.A. / Smith, D.F. / Cummings, R.D. / Paulson, J.C. / Forest, K.T. / Kiessling, L.L.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Data collection / Database references / Derived calculations
Revision 1.3Mar 24, 2021Group: Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Sep 27, 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
Item: _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)68,7588
Polymers68,5172
Non-polymers2406
Water11,854658
1
A: Intelectin-1
hetero molecules

A: Intelectin-1
hetero molecules

A: Intelectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,13612
Polymers102,7763
Non-polymers3619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
B: Intelectin-1
hetero molecules

B: Intelectin-1
hetero molecules

B: Intelectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,13612
Polymers102,7763
Non-polymers3619
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
Unit cell
Length a, b, c (Å)118.450, 118.450, 118.450
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-832-

HOH

21B-802-

HOH

31B-818-

HOH

41B-819-

HOH

51B-821-

HOH

61B-822-

HOH

DetailsThe biological assembly is a trimer. Application of the operations Z,X,Y and Y,Z,X will generate one trimer from the dimer in the asymmetric unit. The peripheral molecules correspond to another distinct trimer.

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Components

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


Mass: 34258.516 Da / Num. of mol.: 2 / Fragment: carbohydrate-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITLN1, INTL, ITLN, LFR, UNQ640/PRO1270 / Plasmid: pcDNA4 / Cell line (production host): HEK293T / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.8→22.2 Å / Num. obs: 51379 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.037 / Rrim(I) all: 0.125 / Χ2: 0.806 / Net I/av σ(I): 19.6 / Net I/σ(I): 5.8 / Num. measured all: 573173
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
1.8-1.8610.10.49550620.9260.1620.5210.566
1.86-1.9411.30.37950850.9630.1180.3970.611
1.94-2.0311.30.28250800.9790.0880.2950.654
2.03-2.1311.30.21551050.9870.0670.2260.715
2.13-2.2711.30.17451250.9910.0540.1830.741
2.27-2.4411.30.16250970.9910.050.170.839
2.44-2.6911.40.14151440.9930.0440.1480.935
2.69-3.0811.30.09951390.9960.0310.1040.854
3.08-3.8711.30.08252030.9960.0260.0861.158
3.87-22.2110.06253390.9970.020.0650.943

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.85 Å22 Å
Translation4.85 Å22 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4WMO

4wmo


Resolution: 1.8→21.996 Å / FOM work R set: 0.9159 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 14.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1639 2519 5.02 %
Rwork0.133 47689 -
obs0.1346 50208 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.82 Å2 / Biso mean: 15.47 Å2 / Biso min: 3.29 Å2
Refinement stepCycle: final / Resolution: 1.8→21.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 6 658 5088
Biso mean--10.05 25.98 -
Num. residues----564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014752
X-RAY DIFFRACTIONf_angle_d1.1076522
X-RAY DIFFRACTIONf_chiral_restr0.085620
X-RAY DIFFRACTIONf_plane_restr0.005859
X-RAY DIFFRACTIONf_dihedral_angle_d14.0331667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8005-1.86480.20122410.14324470471193
1.8648-1.93940.18072470.13954592483995
1.9394-2.02760.19842420.14124685492797
2.0276-2.13450.19172520.13264729498198
2.1345-2.26810.17882510.13164765501698
2.2681-2.4430.15852530.13754773502699
2.443-2.68840.18052540.13714835508999
2.6884-3.07660.16242540.1374856511099
3.0766-3.87270.15172620.127349275189100
3.8727-21.99720.13172630.125850575320100

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