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- PDB-4wmo: Selenomethionine derivative of Xenopus laevis embryonic epidermal... -

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Basic information

Entry
Database: PDB / ID: 4wmo
TitleSelenomethionine derivative of Xenopus laevis embryonic epidermal lectin carbohydrate-binding domain
ComponentsXEEL protein
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate-binding protein / calcium / trimer / fibrinogen-like domain / X-type lectin / innate immunity
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
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 9, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: XEEL protein
C: XEEL protein
B: XEEL protein
D: XEEL protein
E: XEEL protein
A: XEEL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,94538
Polymers191,8886
Non-polymers4,05732
Water26,4821470
1
F: XEEL protein
D: XEEL protein
E: XEEL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,73418
Polymers95,9443
Non-polymers1,79015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-129 kcal/mol
Surface area27820 Å2
MethodPISA
2
C: XEEL protein
B: XEEL protein
A: XEEL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,21120
Polymers95,9443
Non-polymers2,26717
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-126 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.654, 111.069, 123.611
Angle α, β, γ (deg.)90.000, 119.720, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a trimer. There are 2 biological units in the assymetric unit (chains A, B, & C and chain D, E, & F)

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Components

#1: Protein
XEEL protein


Mass: 31981.291 Da / Num. of mol.: 6 / 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: Trichopulsia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q5PPM0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1470 / 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 Å3/Da / Density % sol: 69.26 %
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-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: 2.3→30.4 Å / Num. obs: 129043 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 19.38 Å2 / Rpim(I) all: 0.065 / Rrim(I) all: 0.18 / Rsym value: 0.168 / Χ2: 1.149 / Net I/av σ(I): 13.714 / Net I/σ(I): 4.1 / Num. measured all: 991049
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.387.70.6252.6128850.8970.2410.670.602100
2.38-2.487.70.533128300.9260.2050.5710.624100
2.48-2.597.70.431128490.9510.1650.4620.659100
2.59-2.737.70.331128290.970.1270.3550.737100
2.73-2.97.70.269128510.9780.1030.2880.823100
2.9-3.127.70.215129100.9850.0830.2310.993100
3.12-3.437.70.157129030.9910.060.1681.246100
3.43-3.937.70.11128860.9940.0430.1181.535100
3.93-4.957.60.096129780.9950.0380.1031.953100
4.95-30.47.40.098131220.9940.0390.1052.35599.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.3→30.087 Å / FOM work R set: 0.8737 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.87 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 12676 5 %random
Rwork0.1597 241062 --
obs0.1612 253738 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.24 Å2 / Biso mean: 14.61 Å2 / Biso min: 1.38 Å2
Refinement stepCycle: final / Resolution: 2.3→30.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12834 0 242 1470 14546
Biso mean--40.44 24.36 -
Num. residues----1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113632
X-RAY DIFFRACTIONf_angle_d1.1718593
X-RAY DIFFRACTIONf_chiral_restr0.081829
X-RAY DIFFRACTIONf_plane_restr0.0052401
X-RAY DIFFRACTIONf_dihedral_angle_d15.974895
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 (%)
2.2973-2.37940.267312540.2152238512510598
2.3794-2.47460.241212640.20252418125445100
2.4746-2.58720.225412620.18942413625398100
2.5872-2.72350.209312440.17322415825402100
2.7235-2.8940.219212440.16642421425458100
2.894-3.11720.196112720.15942420125473100
3.1172-3.43060.186412910.15222416225453100
3.4306-3.9260.144112720.13242416625438100
3.926-4.94280.151712980.12672416325461100
4.9428-30.090.173612750.165238302510599

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