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- PDB-4rus: Carp Fishelectin, holo form -

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Basic information

Entry
Database: PDB / ID: 4rus
TitleCarp Fishelectin, holo form
ComponentsFish-egg lectin
KeywordsSUGAR BINDING PROTEIN / six-blade beta propeller / lectin / eggs
Function / homologyTectonin domain / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / carbohydrate binding / extracellular region / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Fish-egg lectin
Function and homology information
Biological speciesCyprinus carpio (common carp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCapaldi, S. / Faggion, B. / Carrizo, M.E. / Destefanis, L. / Gonzalez, M.C. / Perduca, M. / Bovi, M. / Galliano, M. / Monaco, H.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Three-dimensional structure and ligand-binding site of carp fishelectin (FEL).
Authors: Capaldi, S. / Faggion, B. / Carrizo, M.E. / Destefanis, L. / Gonzalez, M.C. / Perduca, M. / Bovi, M. / Galliano, M. / Monaco, H.L.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Fish-egg lectin
B: Fish-egg lectin
C: Fish-egg lectin
D: Fish-egg lectin
E: Fish-egg lectin
F: Fish-egg lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,32633
Polymers152,9756
Non-polymers5,35227
Water14,106783
1
A: Fish-egg lectin
B: Fish-egg lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,87112
Polymers50,9922
Non-polymers1,87910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-8 kcal/mol
Surface area17230 Å2
MethodPISA
2
C: Fish-egg lectin
D: Fish-egg lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,60810
Polymers50,9922
Non-polymers1,6178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-8 kcal/mol
Surface area16950 Å2
MethodPISA
3
E: Fish-egg lectin
F: Fish-egg lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,84711
Polymers50,9922
Non-polymers1,8559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-7 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.410, 120.810, 69.270
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Fish-egg lectin / FEL


Mass: 25495.785 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: eggs / Source: (natural) Cyprinus carpio (common carp) / References: UniProt: P68512

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Sugars , 3 types, 15 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 795 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M N-Acetyl glucosamine, 19% PEG 3350, 0.2 M magnesium formate, 0.05 M Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07156 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2014
RadiationMonochromator: Si(311) and Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07156 Å / Relative weight: 1
ReflectionResolution: 1.7→29.7 Å / Num. all: 171485 / Num. obs: 171485 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.098
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.351 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RUQ

4ruq


Resolution: 1.7→29.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.542 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.11 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21372 8614 5 %RANDOM
Rwork0.19453 ---
all0.1955 162866 --
obs0.1955 162866 93.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.956 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0.62 Å2
2--0.02 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10646 0 345 783 11774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911226
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9715266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82851413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76126.053456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.662151748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2751518
X-RAY DIFFRACTIONr_chiral_restr0.080.21761
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218341
X-RAY DIFFRACTIONr_mcbond_it0.4811.0535670
X-RAY DIFFRACTIONr_mcangle_it0.8631.5747077
X-RAY DIFFRACTIONr_scbond_it0.5631.1465556
X-RAY DIFFRACTIONr_long_range_B_refined3.229.47417975
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 630 -
Rwork0.25 12205 -
obs--94.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.366-0.00210.06340.72780.17080.65380.007-0.0149-0.02310.0191-0.02080.02210.0208-0.0790.01390.0018-0.00490.00650.0472-0.00320.058-24.5869-61.120638.3516
20.6265-0.10070.0750.86610.03020.85430.06240.06710.0253-0.181-0.0556-0.04650.0233-0.0273-0.00680.04570.02440.01240.03520.00690.026-16.6-59.557110.759
30.6984-0.0723-0.13211.03450.56251.05390.04860.1055-0.0783-0.1257-0.08950.1046-0.0415-0.06340.04090.03660.03-0.05610.0323-0.04850.1018-58.2495-46.45316.7394
40.7712-0.38910.13540.8023-0.27621.1879-0.0028-0.0637-0.0950.01110.08670.14740.0279-0.1161-0.08390.00740.0079-0.00590.0319-0.00020.1203-60.0686-36.378733.5256
51.11030.14060.01540.5570.04160.785-0.0416-0.05270.21240.0048-0.0252-0.0041-0.0650.07320.06680.02590.0099-0.03950.04050.00520.1232-21.0901-18.133634.21
60.8182-0.29560.13280.8963-0.29120.72470.02640.16650.1521-0.1196-0.1018-0.06530.02280.09820.07540.0480.0277-0.01420.08420.07010.1071-26.0526-17.45415.9594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION1A301 - 305
3X-RAY DIFFRACTION2B1 - 235
4X-RAY DIFFRACTION2B301 - 305
5X-RAY DIFFRACTION3C1 - 236
6X-RAY DIFFRACTION3C301 - 305
7X-RAY DIFFRACTION4D1 - 237
8X-RAY DIFFRACTION4D301 - 304
9X-RAY DIFFRACTION5E1 - 237
10X-RAY DIFFRACTION5E301 - 305
11X-RAY DIFFRACTION6F1 - 237
12X-RAY DIFFRACTION6F301 - 305

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