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- PDB-4wn0: Xenopus laevis embryonic epidermal lectin in complex with glycero... -

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Basic information

Entry
Database: PDB / ID: 4wn0
TitleXenopus laevis embryonic epidermal lectin in complex with glycerol phosphate
ComponentsXEEL protein
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate-binding protein / calcium / trimer / fibrinogen-like domain / X-type lectin / innate immunity / glycerol phosphate / microbial epitope
Function / homology
Function and homology information


oligosaccharide binding / protein hexamerization / transport vesicle / secretory granule / calcium ion binding / extracellular space / extracellular region
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
SN-GLYCEROL-3-PHOSPHATE / PHOSPHATE ION / Intelectin-1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWangkanont, K. / Kiessling, L.L. / Forest, K.T.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structures of Xenopus Embryonic Epidermal Lectin Reveal a Conserved Mechanism of Microbial Glycan Recognition.
Authors: Wangkanont, K. / Wesener, D.A. / Vidani, J.A. / Kiessling, L.L. / Forest, K.T.
History
DepositionOct 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XEEL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,99310
Polymers31,6531
Non-polymers1,3409
Water3,009167
1
A: XEEL protein
hetero molecules

A: XEEL protein
hetero molecules

A: XEEL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,98030
Polymers94,9593
Non-polymers4,02127
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11140 Å2
ΔGint-137 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.628, 124.628, 55.585
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
DetailsThe biological unit is a trimer generated from the monomer in the asymmetric unit by the operations: -x+y+1, -x, z and -y, x-y-1, z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein XEEL protein


Mass: 31653.029 Da / Num. of mol.: 1 / Fragment: carbohydrate-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XEEL / Plasmid: pFastBac1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q5PPM0

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Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 4.1 Å3/Da / Density % sol: 69.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM Tris-HCl, 20-24% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→30.4 Å / Num. obs: 25366 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 30.89 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.133 / Rsym value: 0.127 / Χ2: 0.925 / Net I/av σ(I): 19.421 / Net I/σ(I): 5.9 / Num. measured all: 285681
Reflection shell

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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.2-2.2811.10.75525260.8660.2370.7920.822
2.28-2.3711.30.63324970.9090.1960.6630.838
2.37-2.4811.40.4925150.9390.1520.5130.851
2.48-2.6111.40.38625240.9650.1190.4040.839
2.61-2.7711.40.27625310.9760.0850.2890.91
2.77-2.9911.40.2125200.9880.0650.220.934
2.99-3.2911.40.13925440.9930.0430.1460.95
3.29-3.7611.40.09725240.9970.030.1011.106
3.76-4.7311.20.06825630.9980.0210.0711.197
4.73-30.410.60.04826220.9980.0160.0510.796

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.72 Å30.2 Å
Translation6.72 Å30.2 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.935 Å / FOM work R set: 0.9043 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 1264 4.99 %random
Rwork0.1515 24092 --
obs0.1524 25356 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.4 Å2 / Biso mean: 25.8 Å2 / Biso min: 11.97 Å2
Refinement stepCycle: final / Resolution: 2.2→29.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 82 167 2388
Biso mean--52.27 33.71 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012307
X-RAY DIFFRACTIONf_angle_d1.0893139
X-RAY DIFFRACTIONf_chiral_restr0.08307
X-RAY DIFFRACTIONf_plane_restr0.005400
X-RAY DIFFRACTIONf_dihedral_angle_d16.631849
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1957-2.28360.23631380.19772616275499
2.2836-2.38740.21881380.1826792817100
2.3874-2.51330.22151400.168926422782100
2.5133-2.67060.19091420.161926742816100
2.6706-2.87670.17151400.148426572797100
2.8767-3.16590.18771390.150626782817100
3.1659-3.62330.14511380.139826832821100
3.6233-4.56240.15951380.12827062844100
4.5624-29.93740.14171510.160127572908100

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