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- PDB-5zc0: Crystal structure of Xenopus embryonic epidermal lectin in comple... -

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Basic information

Entry
Database: PDB / ID: 5zc0
TitleCrystal structure of Xenopus embryonic epidermal lectin in complex with Samarium ions
ComponentsXenopus Embryonic Epidermal Lectin
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding protein / lectin / intelectin / XEEL / Samarium
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
SAMARIUM (III) ION / Intelectin-1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsWangkanont, K.
Funding support Thailand, 3items
OrganizationGrant numberCountry
Chulalongkorn UniversityGDNS 59-059-23-020 Thailand
Chulalongkorn UniversityDNS 61-011-23-003-2 Thailand
Institute for the Promotion of Teaching Science and Technology018/2559 Thailand
CitationJournal: J. Inorg. Biochem. / Year: 2018
Title: Structural stabilities of calcium proteins: Human intelectin-1 and frog lectin XEEL
Authors: Kozak, J.J. / Gray, H.B. / Garza-Lopez, R.A. / Wangkanont, K.
History
DepositionFeb 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xenopus Embryonic Epidermal Lectin
B: Xenopus Embryonic Epidermal Lectin
C: Xenopus Embryonic Epidermal Lectin
D: Xenopus Embryonic Epidermal Lectin
E: Xenopus Embryonic Epidermal Lectin
F: Xenopus Embryonic Epidermal Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,45945
Polymers189,9186
Non-polymers4,54139
Water2,954164
1
A: Xenopus Embryonic Epidermal Lectin
B: Xenopus Embryonic Epidermal Lectin
C: Xenopus Embryonic Epidermal Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,45524
Polymers94,9593
Non-polymers2,49621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-177 kcal/mol
Surface area26810 Å2
MethodPISA
2
D: Xenopus Embryonic Epidermal Lectin
E: Xenopus Embryonic Epidermal Lectin
F: Xenopus Embryonic Epidermal Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,00421
Polymers94,9593
Non-polymers2,04518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-175 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.300, 111.410, 124.360
Angle α, β, γ (deg.)90.000, 119.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Xenopus Embryonic Epidermal Lectin / Embryonic epidermal lectin / Xeel


Mass: 31653.029 Da / Num. of mol.: 6
Fragment: carbohydrate recognition domain, UNP residues 51-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: itln1 / Plasmid: pFastBac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5PPM0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Sm
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.93 Å3/Da / Density % sol: 68.69 % / Mosaicity: 0.62 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM 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: 1.26522 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: 1.26522 Å / Relative weight: 1
ReflectionResolution: 2.75→34.19 Å / Num. obs: 146681 / % possible obs: 97.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 18.81 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.46 / Rpim(I) all: 0.178 / Rrim(I) all: 0.493 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.817.51.84845430.5510.7271.98797
13.47-34.196.80.16360.9910.0420.10992.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.42 Å34.19 Å
Translation7.42 Å34.19 Å

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.6.0phasing
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WN0

4wn0


Resolution: 2.75→34.188 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1
RfactorNum. reflection% reflection
Rfree0.238 7752 5.29 %
Rwork0.1964 --
obs0.1986 146681 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.31 Å2 / Biso mean: 19.0811 Å2 / Biso min: 0.99 Å2
Refinement stepCycle: final / Resolution: 2.75→34.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13050 0 39 164 13253
Biso mean--30.39 13.38 -
Num. residues----1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02413670
X-RAY DIFFRACTIONf_angle_d1.67518360
X-RAY DIFFRACTIONf_chiral_restr0.0961854
X-RAY DIFFRACTIONf_plane_restr0.0122442
X-RAY DIFFRACTIONf_dihedral_angle_d22.7844890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.84830.3149380.2744135021444096
2.8483-2.96220.32246590.2616139921465197
2.9622-3.0970.29987130.2411138021451597
3.097-3.26010.2668820.2351137171459997
3.2601-3.46420.27567560.2283138571461398
3.4642-3.73140.25117080.1924140231473198
3.7314-4.10630.21038950.1627138161471198
4.1063-4.69920.17746810.1438140501473198
4.6992-5.91550.17878150.1564139861480198
5.9155-34.19080.18827050.1656141011480699

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