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- PDB-2c5c: Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 2c5c
TitleShiga-like toxin 1 B subunit complexed with a bivalent inhibitor
ComponentsSHIGA-LIKE TOXIN 1 B SUBUNIT
KeywordsTOXIN / BACTERIAL EXOTOXIN / GB3 BINDING ACTIVITY / BIVALENT LIGAND / PROTEIN-CARBOHYDRATE RECOGNITION / OB FOLD
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
alpha-D-galactopyranose / DIETHYL PROPANE-1,3-DIYLBISCARBAMATE / Shiga-like toxin 1 subunit B / Shiga-like toxin 1 subunit B
Similarity search - Component
Biological speciesBACTERIOPHAGE H30 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsDodd, R.B. / Read, R.J.
CitationJournal: To be Published
Title: Extensive Cross-Linking of the Shiga-Like Toxin 1 B Subunit by a Bivalent Ligand
Authors: Dodd, R.B. / Read, R.J.
History
DepositionOct 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / pdbx_validate_chiral / struct_conn
Item: _atom_site.label_alt_id / _pdbx_validate_chiral.label_alt_id
Revision 2.1Jul 1, 2020Group: Data collection / Other / Category: chem_comp / pdbx_database_status
Item: _chem_comp.type / _pdbx_database_status.status_code_sf
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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_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.type_symbol / _chem_comp.name / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 / _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_symmetry / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHIGA-LIKE TOXIN 1 B SUBUNIT
B: SHIGA-LIKE TOXIN 1 B SUBUNIT
C: SHIGA-LIKE TOXIN 1 B SUBUNIT
D: SHIGA-LIKE TOXIN 1 B SUBUNIT
E: SHIGA-LIKE TOXIN 1 B SUBUNIT
F: SHIGA-LIKE TOXIN 1 B SUBUNIT
G: SHIGA-LIKE TOXIN 1 B SUBUNIT
H: SHIGA-LIKE TOXIN 1 B SUBUNIT
I: SHIGA-LIKE TOXIN 1 B SUBUNIT
J: SHIGA-LIKE TOXIN 1 B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,12440
Polymers76,98610
Non-polymers11,13830
Water32418
1
A: SHIGA-LIKE TOXIN 1 B SUBUNIT
B: SHIGA-LIKE TOXIN 1 B SUBUNIT
C: SHIGA-LIKE TOXIN 1 B SUBUNIT
D: SHIGA-LIKE TOXIN 1 B SUBUNIT
E: SHIGA-LIKE TOXIN 1 B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,11322
Polymers38,4935
Non-polymers6,62017
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
F: SHIGA-LIKE TOXIN 1 B SUBUNIT
G: SHIGA-LIKE TOXIN 1 B SUBUNIT
H: SHIGA-LIKE TOXIN 1 B SUBUNIT
I: SHIGA-LIKE TOXIN 1 B SUBUNIT
J: SHIGA-LIKE TOXIN 1 B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,01118
Polymers38,4935
Non-polymers4,51813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.313, 114.313, 406.936
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
11D-1075-

S10

21I-1075-

S10

31I-1076-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
12B
22C
32D
42E
52F
62G
72H
82J

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRCYSCYSAA1 - 571 - 57
211THRTHRCYSCYSBB1 - 571 - 57
311THRTHRCYSCYSCC1 - 571 - 57
411THRTHRCYSCYSDD1 - 571 - 57
511THRTHRCYSCYSEE1 - 571 - 57
611THRTHRCYSCYSFF1 - 571 - 57
711THRTHRCYSCYSGG1 - 571 - 57
811THRTHRCYSCYSHH1 - 571 - 57
911THRTHRCYSCYSII1 - 571 - 57
1011THRTHRCYSCYSJJ1 - 571 - 57
121ASNASNARGARGAA59 - 6959 - 69
221ASNASNARGARGBB59 - 6959 - 69
321ASNASNARGARGCC59 - 6959 - 69
421ASNASNARGARGDD59 - 6959 - 69
521ASNASNARGARGEE59 - 6959 - 69
621ASNASNARGARGFF59 - 6959 - 69
721ASNASNARGARGGG59 - 6959 - 69
821ASNASNARGARGHH59 - 6959 - 69
921ASNASNARGARGII59 - 6959 - 69
1021ASNASNARGARGJJ59 - 6959 - 69
112HISHISHISHISBB5858
212HISHISHISHISCC5858
312HISHISHISHISDD5858
412HISHISHISHISEE5858
512HISHISHISHISFF5858
612HISHISHISHISGG5858
712HISHISHISHISHH5858
812HISHISHISHISJJ5858

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.91166, 0.04683, 0.40827), (0.36273, 0.37524, -0.85301), (-0.19314, 0.92574, 0.32511)-13.751, 63.27806, -42.65457
2given(0.76974, 0.44027, 0.46224), (0.63166, -0.62995, -0.45186), (0.09225, 0.63979, -0.76299)-40.90538, 118.40041, 4.29065
3given(0.76283, 0.6399, 0.09281), (0.43842, -0.61737, 0.65317), (0.47527, -0.45757, -0.7515)-44.36223, 88.89023, 75.9406
4given(0.9119, 0.36509, -0.18748), (0.0321, 0.39197, 0.91942), (0.40916, -0.84443, 0.34571)-19.03626, 15.66436, 72.56673
5given(-0.81352, -0.52074, 0.25887), (-0.57128, 0.63236, -0.52323), (0.10877, -0.57354, -0.81192)-43.62953, -0.70352, 97.60992
6given(-0.7132, -0.69006, -0.12314), (-0.61522, 0.53204, 0.58175), (-0.33593, 0.49067, -0.80399)-12.31191, -36.22935, -2.66696
7given(-0.80837, -0.40216, -0.42989), (-0.21209, -0.48226, 0.84996), (-0.54914, 0.77826, 0.30455)-26.87077, 48.38424, -74.84479
8given(-0.97141, -0.06117, -0.22939), (0.08516, -0.99171, -0.0962), (-0.2216, -0.11299, 0.96857)-67.2111, 134.93152, -17.59924
9given(-0.96953, -0.14318, 0.19875), (-0.14628, -0.3124, -0.93862), (0.19648, -0.9391, 0.28194)-76.84586, 104.46944, 88.46944

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
SHIGA-LIKE TOXIN 1 B SUBUNIT / VEROTOXIN 1 SUBUNIT B


Mass: 7698.634 Da / Num. of mol.: 10 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 21-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE H30 (virus) / Description: ISOLATED FROM E. COLI O157 H7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69179, UniProt: P69178*PLUS

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Sugars , 5 types, 21 molecules

#2: Polysaccharide
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Polysaccharide
alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(4+1)][a-D-Galp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2112h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 27 molecules

#6: Chemical
ChemComp-S10 / DIETHYL PROPANE-1,3-DIYLBISCARBAMATE


Mass: 218.250 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H18N2O4
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsB-CHAIN IS RESPONSIBLE FOR BINDING THE HOLOTOXIN TO SPECIFIC RECEPTORS ON THE TARGET CELL SURFACE
Sequence detailsPROTEIN IS SYNTHESISED WITH A 20 RESIDUE LEADER SEQUENCE WHICH IS POST-TRANSLATIONALLY CLEAVED.

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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: 2.98 Å3/Da / Density % sol: 58.38 %
Description: 1QNU WAS STRIPPED OF LIGANDS PRIOR TO INPUT AS THE MR SEARCH MODEL. ALTHOUGH THE HIGH RESOLUTION DATA HAVE POOR STATISTICS, AN ANALYSIS OF SIGMAA VALUES INDICATED A SIGNIFICANT ...Description: 1QNU WAS STRIPPED OF LIGANDS PRIOR TO INPUT AS THE MR SEARCH MODEL. ALTHOUGH THE HIGH RESOLUTION DATA HAVE POOR STATISTICS, AN ANALYSIS OF SIGMAA VALUES INDICATED A SIGNIFICANT CORRELATION OF MODEL AND DATA UP TO THE CUT- OFF IMPOSED.
Crystal growpH: 6.5
Details: 32% SATURATED AMMONIUM SULFATE, 2% MPD, 200 MM NACL, 100 MM HEPES [PH 6.5]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2002 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.86→24.04 Å / Num. obs: 196254 / % possible obs: 91.5 % / Observed criterion σ(I): 1.3 / Redundancy: 3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.8
Reflection shellResolution: 2.94→3.04 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.3 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.1.29refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNU

1qnu


Resolution: 2.94→22.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 17.995 / SU ML: 0.315 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFLECTIONS FOR INCLUSION IN THE TEST SET WERE CHOSEN IN THIN RESOLUTION SHELLS TO MITIGATE THE HIGH DEGREE OF NCS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1029 5.1 %RANDOM
Rwork0.198 ---
obs0.201 19087 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.94→22.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5400 0 718 18 6136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0216256
X-RAY DIFFRACTIONr_bond_other_d0.0040.025297
X-RAY DIFFRACTIONr_angle_refined_deg2.4792.0678500
X-RAY DIFFRACTIONr_angle_other_deg1.174312281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.21138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026187
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021132
X-RAY DIFFRACTIONr_nbd_refined0.2090.2921
X-RAY DIFFRACTIONr_nbd_other0.2420.25670
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0980.23477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.53400
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94625520
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.79532856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9524.52980
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1003tight positional0.070.05
12B1003tight positional0.070.05
13C1003tight positional0.060.05
14D1003tight positional0.070.05
15E1003tight positional0.070.05
16F1003tight positional0.060.05
17G1003tight positional0.050.05
18H1003tight positional0.050.05
19I1003tight positional0.060.05
110J1003tight positional0.060.05
21B17tight positional0.030.05
22C17tight positional0.040.05
23D17tight positional0.010.05
24E17tight positional0.030.05
25F17tight positional0.050.05
26G17tight positional0.040.05
27H17tight positional0.060.05
28J17tight positional0.050.05
11A1003tight thermal0.150.5
12B1003tight thermal0.160.5
13C1003tight thermal0.140.5
14D1003tight thermal0.160.5
15E1003tight thermal0.160.5
16F1003tight thermal0.130.5
17G1003tight thermal0.110.5
18H1003tight thermal0.10.5
19I1003tight thermal0.130.5
110J1003tight thermal0.150.5
21B17tight thermal0.160.5
22C17tight thermal0.060.5
23D17tight thermal0.090.5
24E17tight thermal0.120.5
25F17tight thermal0.090.5
26G17tight thermal0.120.5
27H17tight thermal0.110.5
28J17tight thermal0.220.5
LS refinement shellResolution: 2.94→3.02 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.386 75
Rwork0.344 1392
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)
1-0.7302-1.63510.7606-0.1167-1.012.4582-0.0802-0.36260.11410.1642-0.084-0.2416-0.45240.30490.16420.2001-0.1304-0.02830.3165-0.05410.235-25.704860.733239.4554
2-1.10851.28620.37430.00371.0570.9003-0.1562-0.2530.5695-0.13850.27280.0705-0.15940.1872-0.11670.3576-0.13030.00460.14510.05210.3684-27.689174.480623.973
30.06771.18660.79585.15450.3144-1.0708-0.24990.35390.0642-0.73770.3745-0.2536-0.33140.2759-0.12460.2973-0.22190.02420.31020.04880.2191-21.483765.52926.2573
42.9631-1.3915-2.47142.7768-0.11561.2022-0.11380.0716-0.152-0.1180.1920.0352-0.03540.721-0.07820.0302-0.0739-0.05080.3479-0.03350.2338-15.44645.995510.767
52.4362-0.19310.30580.9456-0.3252-0.1247-0.0386-0.0631-0.12080.20780.1128-0.4787-0.01530.1725-0.07420.1112-0.0482-0.07990.2278-0.00260.3142-18.187643.173331.2617
60.84591.3034-0.16052.8788-0.80373.3536-0.25340.91020.0861-0.60580.2570.4727-0.0064-0.3461-0.00350.2725-0.0973-0.070.36940.03380.3865-56.010262.848319.7043
71.9054-0.80881.18510.5495-1.01644.67930.10010.55971.0675-0.01890.33250.6649-0.4517-0.4333-0.43260.388-0.0378-0.03920.35910.22890.9565-64.220981.510824.167
83.14670.76080.4259-1.2202-0.85240.6231-0.1191-0.65261.20270.06450.01380.1072-0.5225-0.48670.10530.57770.10960.03410.4886-0.3361.0232-66.369482.486844.8406
93.4416-0.531-0.5321-0.69061.40561.4120.1054-0.97970.76660.3081-0.19940.342-0.1824-0.15070.0940.3876-0.10490.00120.7246-0.24930.2154-59.295364.545452.8838
101.37210.9364-0.83642.4450.0368-0.07770.0123-0.3398-0.1121-0.18030.00280.34680.0402-0.141-0.01510.1073-0.0584-0.00620.3205-0.07070.2037-52.81152.354237.3868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 69
2X-RAY DIFFRACTION2B1 - 69
3X-RAY DIFFRACTION3C1 - 69
4X-RAY DIFFRACTION4D1 - 69
5X-RAY DIFFRACTION5E1 - 69
6X-RAY DIFFRACTION6F1 - 69
7X-RAY DIFFRACTION7G1 - 69
8X-RAY DIFFRACTION8H1 - 69
9X-RAY DIFFRACTION9I1 - 69
10X-RAY DIFFRACTION10J1 - 69

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