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- PDB-5fsb: Structure of tectonin 2 from laccaria bicolor in complex with 2-o... -

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Basic information

Entry
Database: PDB / ID: 5fsb
TitleStructure of tectonin 2 from laccaria bicolor in complex with 2-o-methyl-methyl-seleno-beta-l-fucopyranoside
ComponentsTECTONIN 2
KeywordsSUGAR BINDING PROTEIN / LECTIN / METHYLATED SUGAR / NEMATOXIC / BETA-PROPELLER
Function / homology: / Tectonin domain / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / carbohydrate binding / methyl 1-seleno-2-O-methyl-beta-L-fucopyranoside / BORIC ACID / Tectonin 2
Function and homology information
Biological speciesLACCARIA BICOLOR (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsSommer, R. / Bleuer, S. / Titz, A. / Kunzler, M. / Varrot, A.
CitationJournal: Structure / Year: 2018
Title: Crystal Structures of Fungal Tectonin in Complex with O-Methylated Glycans Suggest Key Role in Innate Immune Defense.
Authors: Sommer, R. / Makshakova, O.N. / Wohlschlager, T. / Hutin, S. / Marsh, M. / Titz, A. / Kunzler, M. / Varrot, A.
History
DepositionJan 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TECTONIN 2
B: TECTONIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,73618
Polymers47,6262
Non-polymers3,10916
Water9,386521
1
A: TECTONIN 2
hetero molecules

A: TECTONIN 2
hetero molecules

A: TECTONIN 2
B: TECTONIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,47138
Polymers95,2534
Non-polymers6,21834
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
identity operation1_555x,y,z1
MethodPISA
2
A: TECTONIN 2
hetero molecules

A: TECTONIN 2
hetero molecules

A: TECTONIN 2
B: TECTONIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,47138
Polymers95,2534
Non-polymers6,21834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
MethodPISA
3
A: TECTONIN 2
hetero molecules

A: TECTONIN 2
hetero molecules

A: TECTONIN 2
B: TECTONIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,47138
Polymers95,2534
Non-polymers6,21834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.058, 69.058, 349.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-87-

ARG

21B-299-

MG

31A-2009-

HOH

41A-2023-

HOH

51A-2139-

HOH

61A-2140-

HOH

71B-2068-

HOH

81B-2194-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.982, -0.141, 0.124), (-0.164, 0.317, -0.934), (0.092, -0.938, -0.335)
Vector: -4.67992, 32.26551, 46.03787)

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Components

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Protein / Sugars , 2 types, 13 molecules AB

#1: Protein TECTONIN 2


Mass: 23813.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACCARIA BICOLOR (fungus) / Strain: S238N-H82 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0CZL6
#3: Sugar
ChemComp-6YR / methyl 1-seleno-2-O-methyl-beta-L-fucopyranoside / 2-O-methyl-methyl-seleno-L-fucopyranoside / methyl 1-seleno-2-O-methyl-beta-L-fucoside / methyl 1-seleno-2-O-methyl-L-fucoside / methyl 1-seleno-2-O-methyl-fucoside


Type: L-saccharide / Mass: 255.170 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H16O4Se

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Non-polymers , 4 types, 526 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.35 Å3/Da / Density % sol: 47.71 % / Description: NONE
Crystal growpH: 6.5
Details: 1.6M MAGNESIUM SULFATE 0.1M MES PH 6.5. 80% LITHIUM SULFATE WAS USED AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97914
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.65→34.53 Å / Num. obs: 39383 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.65→34.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.716 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. B MOLECULES HAVE THREE STATISTICAL ORIENTATIONS IN THE CRYSTAL AND TO PRODUCE THEM IT WAS CONSTRUCTED AROUND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. B MOLECULES HAVE THREE STATISTICAL ORIENTATIONS IN THE CRYSTAL AND TO PRODUCE THEM IT WAS CONSTRUCTED AROUND TEH THREE FOLD AXIS WITH 0.33 OCCUPANCY DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. MOLECULE B WAS BUILD WITH 0.33 OCCUPANCY TO CREATE BY SYMMETRY THE THREE ORIENTATIONS FOUND IN THE CRYSTAL
RfactorNum. reflection% reflectionSelection details
Rfree0.16656 1983 5 %RANDOM
Rwork0.13306 ---
obs0.13474 37397 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 159 521 4008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023655
X-RAY DIFFRACTIONr_bond_other_d0.0020.023320
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9385025
X-RAY DIFFRACTIONr_angle_other_deg0.91837581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.07223.733150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72715459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2971521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6260.7291830
X-RAY DIFFRACTIONr_mcbond_other0.6240.7281829
X-RAY DIFFRACTIONr_mcangle_it1.0061.0892295
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1780.8911825
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 148 -
Rwork0.169 2695 -
obs--100 %

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