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- PDB-1yae: Structure of the Kainate Receptor Subunit GluR6 Agonist Binding D... -

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Basic information

Entry
Database: PDB / ID: 1yae
TitleStructure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain Complexed with Domoic Acid
ComponentsGlutamate receptor, ionotropic kainate 2
KeywordsMEMBRANE PROTEIN / kainate receptor / glutamate receptor
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / positive regulation of synaptic transmission / behavioral fear response / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / neuron apoptotic process / perikaryon / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DOQ / : / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsNanao, M.H. / Green, T. / Stern-Bach, Y. / Heinemann, S.F. / Choe, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of the kainate receptor subunit GluR6 agonist-binding domain complexed with domoic acid.
Authors: Nanao, M.H. / Green, T. / Stern-Bach, Y. / Heinemann, S.F. / Choe, S.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: 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 / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_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_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.
Remark 999SEQUENCE TRANSMEMBRANE DOMAIN WAS REMOVED AND REPLACED WITH A HYDROPHILIC LINKER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 2
B: Glutamate receptor, ionotropic kainate 2
C: Glutamate receptor, ionotropic kainate 2
D: Glutamate receptor, ionotropic kainate 2
E: Glutamate receptor, ionotropic kainate 2
F: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,93922
Polymers210,7136
Non-polymers4,22616
Water1,40578
1
A: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7983
Polymers35,1191
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8734
Polymers35,1191
Non-polymers7543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8734
Polymers35,1191
Non-polymers7543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8734
Polymers35,1191
Non-polymers7543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8734
Polymers35,1191
Non-polymers7543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6513
Polymers35,1191
Non-polymers5332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
B: Glutamate receptor, ionotropic kainate 2
D: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7458
Polymers70,2382
Non-polymers1,5076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-5 kcal/mol
Surface area25950 Å2
MethodPISA
8
A: Glutamate receptor, ionotropic kainate 2
hetero molecules

A: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5956
Polymers70,2382
Non-polymers1,3574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3930 Å2
ΔGint1 kcal/mol
Surface area24170 Å2
MethodPISA
9
C: Glutamate receptor, ionotropic kainate 2
hetero molecules

E: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7458
Polymers70,2382
Non-polymers1,5076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area3380 Å2
ΔGint0 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.360, 106.570, 172.690
Angle α, β, γ (deg.)90.00, 133.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F
131A
141B
151C
161D
171E
181F
191A
201B
211C
221D
231E
241F
251A
261B
271C
281D
291E
301F
311A
321B
331C
341D
351E
361F
371A
381B
391C
401D
411E
421F
431A
441B
451C
461D
471E
481A
491B
501C
511D
521E
531F
541A
551B
561C
571D
581E
591F
601A
611B
621C
631D
641E
651F
661A
671B
681C
691D
701E
711F
721A
731B
741C
751D
761E
771F
781A
791B
801C
811D
821E
831F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSER5AA423 - 4275 - 9
21ASNASNSERSER5BB423 - 4275 - 9
31ASNASNSERSER5CC423 - 4275 - 9
41ASNASNSERSER5DD423 - 4275 - 9
51ASNASNSERSER5EE423 - 4275 - 9
61ASNASNSERSER5FF423 - 4275 - 9
72LEULEUARGARG5AA428 - 43110 - 13
82LEULEUARGARG5BB428 - 43110 - 13
92LEULEUARGARG5CC428 - 43110 - 13
102LEULEUARGARG5DD428 - 43110 - 13
112LEULEUARGARG5EE428 - 43110 - 13
122LEULEUARGARG5FF428 - 43110 - 13
133SERSERVALVAL2AA432 - 44414 - 26
143SERSERVALVAL2BB432 - 44414 - 26
153SERSERVALVAL2CC432 - 44414 - 26
163SERSERVALVAL2DD432 - 44414 - 26
173SERSERVALVAL2EE432 - 44414 - 26
183SERSERVALVAL2FF432 - 44414 - 26
194LEULEUGLYGLY5AA445 - 46127 - 43
204LEULEUGLYGLY5BB445 - 46127 - 43
214LEULEUGLYGLY5CC445 - 46127 - 43
224LEULEUGLYGLY5DD445 - 46127 - 43
234LEULEUGLYGLY5EE445 - 46127 - 43
244LEULEUGLYGLY5FF445 - 46127 - 43
255GLYGLYLYSLYS3AA461 - 48743 - 69
265GLYGLYLYSLYS3BB461 - 48743 - 69
275GLYGLYLYSLYS3CC461 - 48743 - 69
285GLYGLYLYSLYS3DD461 - 48743 - 69
295GLYGLYLYSLYS3EE461 - 48743 - 69
305GLYGLYLYSLYS3FF461 - 48743 - 69
316TYRTYRGLYGLY3AA488 - 50070 - 82
326TYRTYRGLYGLY3BB488 - 50070 - 82
336TYRTYRGLYGLY3CC488 - 50070 - 82
346TYRTYRGLYGLY3DD488 - 50070 - 82
356TYRTYRGLYGLY3EE488 - 50070 - 82
366TYRTYRGLYGLY3FF488 - 50070 - 82
377METMETLEULEU2AA501 - 54183 - 123
387METMETLEULEU2BB501 - 54183 - 123
397METMETLEULEU2CC501 - 54183 - 123
407METMETLEULEU2DD501 - 54183 - 123
417METMETLEULEU2EE501 - 54183 - 123
427METMETLEULEU2FF501 - 54183 - 123
438ASPASPLYSLYS4AA669 - 679156 - 166
448ASPASPLYSLYS4BB669 - 679156 - 166
458ASPASPLYSLYS4CC669 - 679156 - 166
468ASPASPLYSLYS4DD669 - 679156 - 166
478ASPASPLYSLYS4EE669 - 679156 - 166
489ILEILELYSLYS2AA680 - 695167 - 182
499ILEILELYSLYS2BB680 - 695167 - 182
509ILEILELYSLYS2CC680 - 695167 - 182
519ILEILELYSLYS2DD680 - 695167 - 182
529ILEILELYSLYS2EE680 - 695167 - 182
539ILEILEPHEPHE2FF680 - 694167 - 181
5410LYSLYSVALVAL3AA704 - 716191 - 203
5510LYSLYSVALVAL3BB704 - 716191 - 203
5610LYSLYSVALVAL3CC704 - 716191 - 203
5710LYSLYSVALVAL3DD704 - 716191 - 203
5810LYSLYSVALVAL3EE704 - 716191 - 203
5910LYSLYSSERSER3FF704 - 715191 - 202
6011LEULEUPHEPHE2AA717 - 744204 - 231
6111LEULEUPHEPHE2BB717 - 744204 - 231
6211LEULEUPHEPHE2CC717 - 744204 - 231
6311LEULEUPHEPHE2DD717 - 744204 - 231
6411LEULEUPHEPHE2EE717 - 744204 - 231
6511LEULEUPHEPHE2FF717 - 744204 - 231
6612VALVALGLYGLY3AA745 - 757232 - 244
6712VALVALGLYGLY3BB745 - 757232 - 244
6812VALVALGLYGLY3CC745 - 757232 - 244
6912VALVALGLYGLY3DD745 - 757232 - 244
7012VALVALGLYGLY3EE745 - 757232 - 244
7112VALVALGLYGLY3FF745 - 757232 - 244
7213LEULEUARGARG4AA758 - 800245 - 287
7313LEULEUARGARG4BB758 - 800245 - 287
7413LEULEUARGARG4CC758 - 800245 - 287
7513LEULEUARGARG4DD758 - 800245 - 287
7613LEULEUARGARG4EE758 - 800245 - 287
7713LEULEUARGARG4FF758 - 800245 - 287
7814GLYGLYCYSCYS5AA801 - 804288 - 291
7914GLYGLYCYSCYS5BB801 - 804288 - 291
8014GLYGLYASNASN5CC801 - 802288 - 289
8114GLYGLYCYSCYS5DD801 - 804288 - 291
8214GLYGLYGLYGLY5EE801288
8314ARGARGARGARG5FF800287

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Components

#1: Protein
Glutamate receptor, ionotropic kainate 2 / Kainate receptor / Glutamate receptor 6 / GluR-6 / GluR6 / Excitatory amino acid receptor 4 / EAA4


Mass: 35118.863 Da / Num. of mol.: 6
Fragment: Subunit GLUR6 Agonist Binding Domain with the transmembrane domain removed and replaced with a hydrophilic linker
Source method: isolated from a genetically manipulated source
Details: transmembrane domain was removed and replaced with a hydrophilic linker
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Trichoplusia ni (cabbage looper) / References: GenBank: 56280, UniProt: P42260*PLUS
#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-DOQ / (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID / (2S,3S,4S)-3-CARBOXYMETHYL-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-HEXA-1,3-DIENYL]-PYRROLIDINE-2-CARBOXYLIC ACID / DOMOIC ACID


Mass: 311.330 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H21NO6
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 4.6 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PIPES, Ammonium Sulphate, Ammonium thiocyanate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.1→45 Å / Num. obs: 58030 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.118 / Net I/σ(I): 8.7
Reflection shellResolution: 3.1→3.5 Å / Mean I/σ(I) obs: 2.4 / Num. unique all: 17019 / Rsym value: 0.42 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
XDSdata reduction
XDSdata scaling
PHASERV. 1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTK

1ftk


Resolution: 3.11→45 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.791 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.886 / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33409 2819 5.1 %RANDOM
Rwork0.27545 ---
all0.27846 ---
obs0.27846 52826 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.255 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å2-1 Å2
2--5.91 Å20 Å2
3----5.58 Å2
Refinement stepCycle: LAST / Resolution: 3.11→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12152 0 282 78 12512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212663
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9817070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82851505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01724.213553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.905152316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0671577
X-RAY DIFFRACTIONr_chiral_restr0.1070.21928
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029253
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.26243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.28702
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2458
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.9091.57550
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.335212193
X-RAY DIFFRACTIONr_scbond_it0.84335113
X-RAY DIFFRACTIONr_scangle_it1.4694.54877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A628tight positional0.050.05
2B628tight positional0.050.05
3C628tight positional0.050.05
4D628tight positional0.060.05
5E628tight positional0.050.05
6F628tight positional0.150.05
1A813medium positional0.590.5
2B813medium positional0.570.5
3C813medium positional0.550.5
4D813medium positional0.570.5
5E813medium positional0.620.5
6F813medium positional0.80.5
1A366loose positional1.185
2B366loose positional1.085
3C366loose positional1.15
4D366loose positional1.085
5E366loose positional1.065
6F366loose positional1.695
1A628tight thermal0.080.5
2B628tight thermal0.070.5
3C628tight thermal0.050.5
4D628tight thermal0.050.5
5E628tight thermal0.080.5
6F628tight thermal0.090.5
1A813medium thermal0.512
2B813medium thermal0.442
3C813medium thermal0.372
4D813medium thermal0.352
5E813medium thermal0.42
6F813medium thermal0.732
1A366loose thermal1.8810
2B366loose thermal1.4410
3C366loose thermal1.5510
4D366loose thermal1.5710
5E366loose thermal1.4910
6F366loose thermal1.9610
LS refinement shellResolution: 3.106→3.273 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.422 364 -
Rwork0.369 7390 -
obs--90.48 %

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