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- PDB-5xfd: Serial femtosecond X-ray structure of Agrocybe cylindracea galect... -

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Entry
Database: PDB / ID: 5xfd
TitleSerial femtosecond X-ray structure of Agrocybe cylindracea galectin with lactose solved by Se-SAD using XFEL (refined against 60,000 patterns)
ComponentsGalactoside-binding lectin
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Blood group A H type 2 antigen, alpha anomer / Galectin
Similarity search - Component
Biological speciesAgrocybe cylindracea (fungus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 1.5 Å
AuthorsKuwabara, N. / Fumiaki, Y. / Kato, R.
CitationJournal: IUCrJ / Year: 2017
Title: Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
Authors: Yamashita, K. / Kuwabara, N. / Nakane, T. / Murai, T. / Mizohata, E. / Sugahara, M. / Pan, D. / Masuda, T. / Suzuki, M. / Sato, T. / Kodan, A. / Yamaguchi, T. / Nango, E. / Tanaka, T. / ...Authors: Yamashita, K. / Kuwabara, N. / Nakane, T. / Murai, T. / Mizohata, E. / Sugahara, M. / Pan, D. / Masuda, T. / Suzuki, M. / Sato, T. / Kodan, A. / Yamaguchi, T. / Nango, E. / Tanaka, T. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Manya, H. / Endo, T. / Kato, R. / Senda, T. / Kato, H. / Iwata, S. / Ago, H. / Yamamoto, M. / Yumoto, F. / Nakatsu, T.
History
DepositionApr 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_validate_close_contact / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_molecule_features ...atom_site / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
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_seq_id / _atom_site.label_asym_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order
Revision 3.1Oct 14, 2020Group: Structure summary / Category: chem_comp / pdbx_molecule / Item: _chem_comp.pdbx_synonyms
Revision 3.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactoside-binding lectin
B: Galactoside-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7554
Polymers38,2902
Non-polymers1,4652
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.795, 105.795, 75.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Galactoside-binding lectin


Mass: 19144.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe cylindracea (fungus) / Plasmid: pET27b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCI3*PLUS
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Blood group A H type 2 antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5 / Details: PEG1500

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 0.954 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.5→9.5 Å / Num. obs: 150810 / % possible obs: 100 % / Redundancy: 443.377 % / CC1/2: 0.9902844 / Net I/σ(I): 6.460021
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
3.088-9.497742.112.72167910.98461100
2.465-3.088616.411.310.98651100
2.157-2.4655629.870.98421100
1.962-2.1574617.890.97761100
1.823-1.962438.45.890.96451100
1.716-1.823399.54.060.91791100
1.631-1.716333.82.850.841100
1.56-1.631258.52.110.72011100
1.5-1.561791.450.54211100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
CrystFELdata reduction
CrystFELdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→9.489 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.46
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1625 7399 4.91 %
Rwork0.1488 --
obs0.1495 150732 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.26 Å2 / Biso mean: 24.3006 Å2 / Biso min: 11.11 Å2
Refinement stepCycle: final / Resolution: 1.5→9.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 100 232 2649
Biso mean--22.61 40.18 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192589
X-RAY DIFFRACTIONf_angle_d1.4783565
X-RAY DIFFRACTIONf_chiral_restr0.121459
X-RAY DIFFRACTIONf_plane_restr0.008448
X-RAY DIFFRACTIONf_dihedral_angle_d11.9091536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.5170.28222480.279947955043
1.517-1.53480.24582620.266247915053
1.5348-1.55340.27322280.258247494977
1.5534-1.5730.24692580.238848175075
1.573-1.59360.22312760.235147114987
1.5936-1.61530.23982210.229148195040
1.6153-1.63830.21932600.213447615021
1.6383-1.66260.23942070.208348295036
1.6626-1.68840.20312390.198148005039
1.6884-1.7160.2032290.186347484977
1.716-1.74540.20351980.182548435041
1.7454-1.77690.17622720.167647525024
1.7769-1.81090.19572390.159648025041
1.8109-1.84760.18522690.159247194988
1.8476-1.88740.16872380.158348315069
1.8874-1.9310.16332410.150347514992
1.931-1.97880.13292600.141747625022
1.9788-2.03180.17172600.13947715031
2.0318-2.0910.15872520.139747895041
2.091-2.15770.14922710.139547535024
2.1577-2.23390.15832270.13347534980
2.2339-2.32210.14262570.134447685025
2.3221-2.42610.15732690.143247685037
2.4261-2.55160.17282260.145547895015
2.5516-2.7080.1552550.143148125067
2.708-2.91150.15162380.145947474985
2.9115-3.19430.19212380.140947935031
3.1943-3.63360.12912480.125247835031
3.6336-4.49540.13112540.1247745028
4.4954-9.48880.15172590.136847535012
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)
12.68770.9696-1.06865.9803-3.05894.9666-0.0038-0.0247-0.05080.15920.16290.47050.1411-0.2454-0.0560.15910.00070.02720.1147-0.01140.1971-60.86646.014511.9477
21.28660.0740.17891.72510.22091.11670.0490.09060.1415-0.10230.0211-0.0179-0.05970.0582-0.05550.1610.00720.01680.119-0.00180.1282-48.108516.48458.0505
31.76-0.1147-0.07084.37891.68592.6520.0076-0.11680.0577-0.04890.1134-0.1842-0.0380.2709-0.12790.132-0.02650.00060.13940.00950.1507-40.257720.886912.3826
42.7860.2614-0.17272.2983-1.14574.60380.01660.0971-0.2155-0.0177-0.1021-0.19840.5130.50120.03290.19240.0397-0.00210.1424-0.00350.1717-45.23346.03811.2665
52.3668-0.1472-0.05314.29691.79812.89580.0403-0.0869-0.03540.21660.0201-0.36570.09640.1756-0.10080.17820.0094-0.01210.14080.00760.1755-41.14579.020115.9789
62.38440.21170.23572.21271.122.72150.09240.07680.1572-0.0919-0.06360.0302-0.2446-0.13540.02620.15040.01580.01580.07210.0080.1512-51.37718.38989.9228
70.79921.1071-1.90863.0608-4.37569.88630.05710.02160.0583-0.11980.00330.28430.41210.1416-0.1160.17830.01260.0140.1319-0.0050.154-56.22956.083711.7263
81.3904-0.0050.22642.631-0.02661.12710.0199-0.0554-0.02830.06240.0209-0.3091-0.04920.1461-0.00610.14740.0040.00220.13170.01120.1687-45.9901-8.892712.9924
91.6306-0.5242-0.98623.5788-0.96171.1570.06810.3368-0.064-0.43940.0710.21520.1822-0.1553-0.37130.21820.0105-0.01660.1750.00310.1471-58.9938-9.1493.4102
102.18410.6409-0.454.179-1.01361.4877-0.01680.013-0.1724-0.01610.04060.05360.0488-0.0225-0.03020.15320.0030.00280.1111-0.0010.1638-59.963-20.99813.0085
111.98390.6313-0.89074.9874-2.68393.9180.2090.16760.2833-0.11050.02650.867-0.3179-0.1642-0.32440.23120.0477-0.04250.27210.01530.3398-69.6431-9.19136.1267
123.1067-0.79381.19262.73990.18551.9828-0.0055-0.14180.08730.1535-0.01040.1317-0.1261-0.12770.03630.16920.00770.020.09710.00240.1575-60.0889-5.842215.4412
131.69970.3072-0.58542.1342-0.62960.5440.0794-0.1739-0.15940.2446-0.04170.2183-0.00660.00210.04850.2252-0.01170.02460.14640.00850.1712-59.2684-13.529920.0474
142.9827-1.2179-0.50124.0574-1.82821.32350.14090.2928-0.1628-0.4749-0.0090.10290.2798-0.0888-0.18750.22930.00760.00480.1565-0.0160.1602-55.0726-15.46542.8153
151.26060.66932.48521.09411.23945.78710.0553-0.0034-0.07590.04740.0775-0.2275-0.2280.1554-0.1860.21740.00070.00480.14450.0040.1652-49.0217-4.293312.3341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 12 )A2 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 75 )A13 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 96 )A76 - 96
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 112 )A97 - 112
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 127 )A113 - 127
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 150 )A128 - 150
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 161 )A151 - 161
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 27 )B2 - 27
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 47 )B28 - 47
10X-RAY DIFFRACTION10chain 'B' and (resid 48 through 86 )B48 - 86
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 102 )B87 - 102
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 120 )B103 - 120
13X-RAY DIFFRACTION13chain 'B' and (resid 121 through 135 )B121 - 135
14X-RAY DIFFRACTION14chain 'B' and (resid 136 through 150 )B136 - 150
15X-RAY DIFFRACTION15chain 'B' and (resid 151 through 161 )B151 - 161

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