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- PDB-5ojm: Structure of a chimaeric beta3-alpha5 GABAA receptor in complex w... -

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Basic information

Entry
Database: PDB / ID: 5ojm
TitleStructure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25
Components
  • Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5
  • Nanobody Nb25
KeywordsMEMBRANE PROTEIN / GABAA receptor / Nanobody complex / Neurosteroid / Ion channel
Function / homology
Function and homology information


inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / GABA receptor binding / innervation ...inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / GABA receptor binding / innervation / postsynaptic specialization membrane / neurotransmitter receptor activity / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / neuronal cell body membrane / cochlea development / roof of mouth development / Signaling by ERBB4 / associative learning / chloride channel complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / behavioral fear response / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / signaling receptor activity / presynaptic membrane / postsynapse / postsynaptic membrane / neuron projection / synapse / signal transduction / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. ...Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit beta-3 / Gamma-aminobutyric acid receptor subunit alpha-5
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMiller, P.S. / Scott, S. / Masiulis, S. / De Colibus, L. / Pardon, E. / Steyaert, J. / Aricescu, A.R.
Funding support United Kingdom, France, 6items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M024709/1 United Kingdom
Medical Research Council (United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (United Kingdom)MC_UP_1201/15 United Kingdom
Wellcome Trust105247/Z/14/Z United Kingdom
Human Frontier Science ProgramRGP0065/2014 France
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis for GABAA receptor potentiation by neurosteroids.
Authors: Miller, P.S. / Scott, S. / Masiulis, S. / De Colibus, L. / Pardon, E. / Steyaert, J. / Aricescu, A.R.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / 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 / _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.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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5
B: Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5
C: Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5
D: Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5
E: Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5
K: Nanobody Nb25
L: Nanobody Nb25
M: Nanobody Nb25
N: Nanobody Nb25
O: Nanobody Nb25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,51620
Polymers290,53210
Non-polymers5,98410
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45170 Å2
ΔGint-48 kcal/mol
Surface area85560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.350, 139.940, 191.500
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12A
22D
13A
23C
14A
24B
15E
25D
16E
26C
17E
27B
18D
28C
19D
29B
110C
210B
111K
211L
112K
212M
113K
213N
114K
214O
115L
215M
116L
216N
117L
217O
118M
218N
119M
219O
120N
220O

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHELEULEUAA11 - 41842 - 371
21PHEPHELEULEUEE11 - 41842 - 371
12PHEPHETYRTYRAA11 - 41742 - 370
22PHEPHETYRTYRDD11 - 41742 - 370
13PHEPHELEULEUAA11 - 41842 - 371
23PHEPHELEULEUCC11 - 41842 - 371
14PHEPHETYRTYRAA11 - 41742 - 370
24PHEPHETYRTYRBB11 - 41742 - 370
15PHEPHETYRTYREE11 - 41742 - 370
25PHEPHETYRTYRDD11 - 41742 - 370
16PHEPHELEULEUEE11 - 41842 - 371
26PHEPHELEULEUCC11 - 41842 - 371
17PHEPHETYRTYREE11 - 41742 - 370
27PHEPHETYRTYRBB11 - 41742 - 370
18PHEPHETYRTYRDD11 - 41742 - 370
28PHEPHETYRTYRCC11 - 41742 - 370
19METMETTYRTYRDD9 - 41740 - 370
29METMETTYRTYRBB9 - 41740 - 370
110PHEPHETYRTYRCC11 - 41742 - 370
210PHEPHETYRTYRBB11 - 41742 - 370
111GLNGLNVALVALKF1 - 1231 - 123
211GLNGLNVALVALLG1 - 1231 - 123
112GLNGLNVALVALKF1 - 1231 - 123
212GLNGLNVALVALMH1 - 1231 - 123
113GLNGLNVALVALKF1 - 1231 - 123
213GLNGLNVALVALNI1 - 1231 - 123
114GLNGLNVALVALKF1 - 1231 - 123
214GLNGLNVALVALOJ1 - 1231 - 123
115GLNGLNVALVALLG1 - 1231 - 123
215GLNGLNVALVALMH1 - 1231 - 123
116GLNGLNVALVALLG1 - 1231 - 123
216GLNGLNVALVALNI1 - 1231 - 123
117GLNGLNVALVALLG1 - 1231 - 123
217GLNGLNVALVALOJ1 - 1231 - 123
118GLNGLNVALVALMH1 - 1231 - 123
218GLNGLNVALVALNI1 - 1231 - 123
119GLNGLNVALVALMH1 - 1231 - 123
219GLNGLNVALVALOJ1 - 1231 - 123
120GLNGLNVALVALNI1 - 1231 - 123
220GLNGLNVALVALOJ1 - 1231 - 123

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

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Components

#1: Protein
Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5 / GABA(A) receptor subunit beta-3 / GABA(A) receptor subunit alpha-5


Mass: 44433.367 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: This is a chimaeric construct, containing the secretion signal sequence from pHLsec vector (PMID: 17001101), the extracellular region of h uman GBRB3 (mature polypeptide residues 1-217 from ...Details: This is a chimaeric construct, containing the secretion signal sequence from pHLsec vector (PMID: 17001101), the extracellular region of h uman GBRB3 (mature polypeptide residues 1-217 from Uniprot P28472), the transmembrane region from human GBRA5 (mature polypeptide residues 226-431 from Uniprot P31644 with the exception of the M3-M4 loop, residues 316-392, which were substituted by SQPARAA) and a C-terminal R ho-1D4 purification tag (TETSQVAPA).
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Homo sapiens (human)
Plasmid: pHLsec / Gene: GABRB3, GABRA5 / Cell line (production host): HEK-293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P28472, UniProt: P31644
#2: Antibody
Nanobody Nb25


Mass: 13673.024 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMESy4 / Production host: Escherichia coli (E. coli)
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 14% poly-ethylene glycol (PEG) 5000, 0.08M magnesium acetate, 0.1M sodium citrate, 1mM ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→48.88 Å / Num. obs: 68852 / % possible obs: 99.78 % / Redundancy: 10 % / Biso Wilson estimate: 87.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.352 / Rpim(I) all: 0.116 / Net I/σ(I): 7.85
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 9.9 % / Rmerge(I) obs: 2.807 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 6886 / CC1/2: 0.395 / Rpim(I) all: 0.935 / % possible all: 99.71

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Processing

Software
NameVersionClassification
HKL-2000708cdata reduction
Aimless0.5.25data scaling
PHASER2.5.7phasing
REFMAC5.8.0158refinement
PHENIX(1.12rc)-2787-000)refinement
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4COF

4cof


Resolution: 3.3→48.88 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.809 / SU B: 52.621 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.574 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 2506 4.9 %RANDOM
Rwork0.2337 ---
obs0.23449 48360 73.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.037 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å21.92 Å2
2---1.67 Å20 Å2
3---2.77 Å2
Refinement stepCycle: 1 / Resolution: 3.3→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18141 0 397 0 18538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01919035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217413
X-RAY DIFFRACTIONr_angle_refined_deg0.711.93725863
X-RAY DIFFRACTIONr_angle_other_deg0.501340161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23652260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36822.747841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.586153014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.69715140
X-RAY DIFFRACTIONr_chiral_restr0.0540.22935
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0220769
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024255
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_it2.2353.3529070
X-RAY DIFFRACTIONr_mcbond_other2.2353.3529069
X-RAY DIFFRACTIONr_mcangle_it3.6825.02611320
X-RAY DIFFRACTIONr_mcangle_other3.6825.02611321
X-RAY DIFFRACTIONr_scbond_it2.6773.6739965
X-RAY DIFFRACTIONr_scbond_other2.6773.6739966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.375.4214544
X-RAY DIFFRACTIONr_long_range_B_refined8.76364.24677427
X-RAY DIFFRACTIONr_long_range_B_other8.76364.24677428
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A223120.06
12E223120.06
21A221960.06
22D221960.06
31A221460.07
32C221460.07
41A221740.07
42B221740.07
51E222320.06
52D222320.06
61E222620.07
62C222620.07
71E222980.06
72B222980.06
81D222920.06
82C222920.06
91D222540.06
92B222540.06
101C221300.06
102B221300.06
111K74700.01
112L74700.01
121K74540.03
122M74540.03
131K74620.03
132N74620.03
141K74460.04
142O74460.04
151L74600.03
152M74600.03
161L74600.03
162N74600.03
171L74460.04
172O74460.04
181M74900.01
182N74900.01
191M74900.02
192O74900.02
201N74800.02
202O74800.02
LS refinement shellResolution: 3.296→3.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 9 -
Rwork0.277 242 -
obs--4.96 %
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)
10.6334-0.10260.66870.64210.5093.43950.05640.1907-0.0717-0.2170.0023-0.07930.5050.327-0.05870.4605-0.0370.00150.0959-0.00490.0454-17.2155-168.1172405.7353
20.7431-0.09730.43930.40640.05553.5788-0.10610.2350.1431-0.2335-0.0743-0.13350.02720.4560.18040.2625-0.04860.0650.15240.0660.0667-7.8859-144.95403.3235
30.5241-0.12630.74420.5006-0.38944.3256-0.12960.04190.1909-0.1966-0.0643-0.0121-0.3441-0.20890.1940.31220.0027-0.08260.04590.02310.0771-26.5419-128.6464407.7648
40.6537-0.12910.81640.5897-0.23563.1171-0.1138-0.08890.096-0.2017-0.04810.1960.0164-0.93220.16190.1645-0.039-0.12860.50550.00450.1375-47.1609-141.8598413.2392
50.7933-0.03010.92440.54520.04593.1422-0.0021-0.0518-0.0847-0.1927-0.0720.15050.583-0.62360.07410.504-0.3154-0.13170.28530.03230.122-41.3379-166.3512411.4354
65.49471.3078-0.47694.2269-0.43550.4584-0.0627-0.512-1.0376-0.13380.09450.19130.5253-0.2834-0.03180.9903-0.3185-0.16130.44050.08120.3706-34.1842-194.2836406.3735
71.7662-0.869-1.26395.6655-1.04041.6173-0.3375-0.0871-0.04831.26710.59751.3999-0.2007-0.5932-0.260.77710.0088-0.10671.56440.02770.7401-71.4301-158.5935415.5667
84.84050.9859-1.65295.82-0.52151.15580.4447-0.32870.80240.5694-0.27570.2002-0.7276-0.0682-0.1690.75460.1515-0.12840.56710.04160.3413-49.734-110.7844409.9742
94.37880.1156-1.65264.35670.93612.1460.0068-0.62720.6257-0.30530.2124-0.9262-0.41741.1114-0.21910.6314-0.24910.09320.74450.0660.42790.7139-117.3412397.3023
103.6151-0.5882-0.93586.62641.0750.5001-0.017-0.0462-0.36130.1151-0.011-0.73890.23870.18840.0280.57030.09650.14430.4808-0.02370.353210.0034-169.0388395.1556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 3008
2X-RAY DIFFRACTION2E11 - 3008
3X-RAY DIFFRACTION3D9 - 3008
4X-RAY DIFFRACTION4C11 - 3008
5X-RAY DIFFRACTION5B8 - 3008
6X-RAY DIFFRACTION6K1 - 123
7X-RAY DIFFRACTION7L1 - 123
8X-RAY DIFFRACTION8M1 - 123
9X-RAY DIFFRACTION9N1 - 123
10X-RAY DIFFRACTION10O1 - 123

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