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- PDB-6hmy: Cholera toxin classical B-pentamer in complex with fucosyl-GM1 -

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Basic information

Entry
Database: PDB / ID: 6hmy
TitleCholera toxin classical B-pentamer in complex with fucosyl-GM1
ComponentsCholera enterotoxin B-subunit
KeywordsTOXIN / cholera toxin / lectin / complex / fucosyl-GM1 / protein-carbohydrate interactions / X-ray crystal structure
Function / homology
Function and homology information


host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / catalytic complex / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / metal ion binding / membrane
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Cholera enterotoxin subunit B / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKrengel, U. / Heim, J.B.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway247730 Norway
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structures of cholera toxin in complex with fucosylated receptors point to importance of secondary binding site.
Authors: Heim, J.B. / Hodnik, V. / Heggelund, J.E. / Anderluh, G. / Krengel, U.
History
DepositionSep 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / 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 / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn / struct_conn_type / 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_alt_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.pdbx_formal_charge / _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_alt_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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 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
Revision 3.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
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.id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_close_contact.label_alt_id_1 / _pdbx_validate_close_contact.label_alt_id_2 / _struct_asym.entity_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholera enterotoxin B-subunit
B: Cholera enterotoxin B-subunit
C: Cholera enterotoxin B-subunit
D: Cholera enterotoxin B-subunit
E: Cholera enterotoxin B-subunit
F: Cholera enterotoxin B-subunit
G: Cholera enterotoxin B-subunit
H: Cholera enterotoxin B-subunit
I: Cholera enterotoxin B-subunit
J: Cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,04442
Polymers116,23310
Non-polymers13,81132
Water14,358797
1
A: Cholera enterotoxin B-subunit
B: Cholera enterotoxin B-subunit
C: Cholera enterotoxin B-subunit
D: Cholera enterotoxin B-subunit
E: Cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,85820
Polymers58,1165
Non-polymers6,74115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Cholera enterotoxin B-subunit
G: Cholera enterotoxin B-subunit
H: Cholera enterotoxin B-subunit
I: Cholera enterotoxin B-subunit
J: Cholera enterotoxin B-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,18622
Polymers58,1165
Non-polymers7,07017
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.626, 74.137, 111.245
Angle α, β, γ (deg.)90.00, 105.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Cholera enterotoxin B-subunit / Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera ...Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera toxin beta subunit / Cholera toxin subunit B / Cholerae toxin B subunit / CtxB


Mass: 11623.267 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ctxB, C9J66_18955, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193, UniProt: P01556*PLUS

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Sugars , 4 types, 12 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1145.026 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-4-2-5/a4-b1_b3-c2_b4-d1_d3-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1145.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-4-2-5/a4-b1_b3-c2_b4-d1_d3-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1145.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-4-2-5/a4-b1_b3-c2_b4-d1_d3-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 817 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 0.1 M Bicine-Tris, 6% PEG1000, 6% PEG3350, 6% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.980802 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980802 Å / Relative weight: 1
ReflectionResolution: 1.6→44.32 Å / Num. obs: 150674 / % possible obs: 98.4 % / Redundancy: 2.6 % / Rrim(I) all: 0.176 / Net I/σ(I): 4.9
Reflection shellResolution: 1.6→1.63 Å / CC1/2: 0.449 / Rrim(I) all: 0.964

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELB

5elb


Resolution: 1.6→44.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.397 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21414 7592 5 %RANDOM
Rwork0.18364 ---
obs0.18517 143082 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.23 Å2
2--0.67 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.6→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8140 0 922 797 9859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01410379
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179317
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.71414305
X-RAY DIFFRACTIONr_angle_other_deg0.9981.65522260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.3035.2061211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83623.437451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.486151729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8721531
X-RAY DIFFRACTIONr_chiral_restr0.0830.21820
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210843
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021585
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_it0.4810.5684375
X-RAY DIFFRACTIONr_mcbond_other0.480.5684374
X-RAY DIFFRACTIONr_mcangle_it0.8120.8475529
X-RAY DIFFRACTIONr_mcangle_other0.8120.8475530
X-RAY DIFFRACTIONr_scbond_it0.660.676004
X-RAY DIFFRACTIONr_scbond_other0.660.676004
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.050.9798719
X-RAY DIFFRACTIONr_long_range_B_refined3.8628.03210687
X-RAY DIFFRACTIONr_long_range_B_other3.8628.03310688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 566 -
Rwork0.305 10508 -
obs--98.42 %
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)
11.30070.1491-0.43550.9624-0.12531.69840.022-0.12490.08520.13220.00020.0138-0.06920.0066-0.02230.0771-0.0009-0.00480.0166-0.02330.073-40.054-5.706448.181
20.7467-0.00870.06361.5425-0.22431.1583-0.0119-0.131-0.04920.117-0.00540.00120.05870.00760.01730.0782-0.00120.00490.03020.00070.0387-42.9509-28.030950.8955
31.7654-0.0966-0.41190.94250.11350.9841-0.0368-0.034-0.1338-0.0008-0.0098-0.08740.12870.08650.04660.08590.0094-0.00720.00960.01510.0749-29.1695-38.687336.4718
41.6540.2553-0.06681.2957-0.04960.72750.00410.0248-0.0138-0.02640.021-0.0837-0.00780.0753-0.02510.05440.0127-0.0040.0127-0.00920.0427-17.8835-22.864224.7738
51.26650.0399-0.02061.32940.36791.25340.0147-0.07280.15630.02690.0036-0.0239-0.12930.0376-0.01830.0614-0.01270.00040.0076-0.0020.0695-24.5239-2.494631.9928
61.08-0.45270.4191.5095-0.24790.7844-0.0047-0.08210.04030.02950.01310.0121-0.0341-0.0581-0.00830.0364-0.00510.00180.02190.00670.0376-70.2629-8.864423.3174
70.9697-0.04280.02510.6449-0.37241.51490.01010.05620.0784-0.03910.002-0.0377-0.06320.0403-0.01210.04970.0021-0.00770.00520.00470.0651-55.6854-0.79597.9455
80.9441-0.21320.11541.37810.47921.1590.02510.1313-0.0695-0.1105-0.0292-0.02010.02630.06060.00410.06820.0112-0.00430.04940.00090.047-45.4605-18.2219-2.2896
91.27850.2945-0.09831.0936-0.09231.20550.02330.1031-0.1631-0.0581-0.02450.06940.1345-0.05610.00120.08180.0135-0.01880.0335-0.03420.0859-54.1326-37.29456.4622
102.3339-0.1043-0.19870.45950.13860.53020.0268-0.0241-0.09920.04940.02450.05030.0531-0.0472-0.05140.0816-0.0198-0.02530.01220.01910.072-69.3306-31.565522.3637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 201
2X-RAY DIFFRACTION2B1 - 301
3X-RAY DIFFRACTION3C1 - 301
4X-RAY DIFFRACTION4D1 - 301
5X-RAY DIFFRACTION5E1 - 301
6X-RAY DIFFRACTION6F1 - 401
7X-RAY DIFFRACTION7G1 - 301
8X-RAY DIFFRACTION8H1 - 301
9X-RAY DIFFRACTION9I1 - 301
10X-RAY DIFFRACTION10J1 - 401

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