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- PDB-5fsc: Structure of tectonin 2 from Laccaria bicolor in complex with all... -

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Basic information

Entry
Database: PDB / ID: 5fsc
TitleStructure of tectonin 2 from Laccaria bicolor in complex with allyl- alpha_4-methyl-mannoside
ComponentsTECTONIN 2
KeywordsSUGAR BINDING PROTEIN / LECTIN / METHYLATED SUGAR / NEMATOXIC / BETA-PROPELLER
Function / homologyTectonin domain / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / prop-2-en-1-yl 4-O-methyl-alpha-D-mannopyranoside / Tectonin 2
Function and homology information
Biological speciesLACCARIA BICOLOR (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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 1.4Jan 10, 2024Group: 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: TECTONIN 2
B: TECTONIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,78313
Polymers47,6262
Non-polymers2,15711
Water9,260514
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)98,86423
Polymers95,2534
Non-polymers3,61119
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)98,86423
Polymers95,2534
Non-polymers3,61119
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)98,86423
Polymers95,2534
Non-polymers3,61119
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)69.007, 69.007, 348.953
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-299-

MG

21A-2009-

HOH

31A-2025-

HOH

41A-2158-

HOH

51A-2169-

HOH

61A-2279-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.983, -0.138, 0.12), (-0.159, 0.317, -0.935), (0.091, -0.938, -0.334)
Vector: -4.49687, 32.33266, 46.0523)

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Sugar
ChemComp-G8Z / prop-2-en-1-yl 4-O-methyl-alpha-D-mannopyranoside / Allyl-Alpha-4-Methyl-Mannoside / prop-2-en-1-yl 4-O-methyl-alpha-D-mannoside / prop-2-en-1-yl 4-O-methyl-D-mannoside / prop-2-en-1-yl 4-O-methyl-mannoside


Type: D-saccharide / Mass: 234.246 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C10H18O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 1.3M MAGNESIUM SULFATE 0.1M MES PH 6.5 80% LITHIUM FORMATE WAS USED AS CROPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625
DetectorType: RAYONIX / Detector: CCD / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→38.77 Å / Num. obs: 24046 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FSB

5fsb


Resolution: 1.95→38.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.969 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY SOME DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. THERE ARE THREE STATISTICAL ORIENTATION OF MOLECULE B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY SOME DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. THERE ARE THREE STATISTICAL ORIENTATION OF MOLECULE B FORMING A THREE FOLD AXIS. MOLECULE B WAS BUILD AROUND THE THREE FOLD AXIS WITH 0.33 OCCUPANCY TO OBTAIN THOSE ORIENTATIONS BY SYMMETRY
RfactorNum. reflection% reflectionSelection details
Rfree0.18476 1141 4.7 %RANDOM
Rwork0.14566 ---
obs0.14752 22904 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 146 514 3989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023640
X-RAY DIFFRACTIONr_bond_other_d0.0020.023323
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9364987
X-RAY DIFFRACTIONr_angle_other_deg1.2937580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.25823.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20715466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6671520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024221
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02901
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_it0.370.6361828
X-RAY DIFFRACTIONr_mcbond_other0.3690.6361827
X-RAY DIFFRACTIONr_mcangle_it0.6210.9512292
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7110.7541812
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 96 -
Rwork0.168 1644 -
obs--99.94 %

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