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- PDB-6e7t: Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal dom... -

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Basic information

Entry
Database: PDB / ID: 6e7t
TitleHeterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / NMDA Receptor / Ion channel / Allosteric modulation / Extracellular domain
Function / homology
Function and homology information


neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / NMDA selective glutamate receptor signaling pathway / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / EPHB-mediated forward signaling / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration ...neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / NMDA selective glutamate receptor signaling pathway / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / EPHB-mediated forward signaling / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Assembly and cell surface presentation of NMDA receptors / regulation of protein kinase A signaling / dendritic branch / apical dendrite / response to other organism / fear response / response to methylmercury / positive regulation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity / cellular response to dsRNA / regulation of monoatomic cation transmembrane transport / response to carbohydrate / negative regulation of dendritic spine maintenance / interleukin-1 receptor binding / cellular response to lipid / positive regulation of glutamate secretion / NMDA glutamate receptor activity / response to growth hormone / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / protein heterotetramerization / glutamate binding / action potential / glycine binding / response to zinc ion / heterocyclic compound binding / suckling behavior / receptor clustering / startle response / behavioral response to pain / regulation of neuronal synaptic plasticity / response to amine / monoatomic cation transmembrane transport / regulation of MAPK cascade / small molecule binding / associative learning / positive regulation of excitatory postsynaptic potential / response to magnesium ion / monoatomic cation transport / extracellularly glutamate-gated ion channel activity / cellular response to organic cyclic compound / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / regulation of postsynaptic membrane potential / multicellular organismal response to stress / behavioral fear response / cellular response to manganese ion / D2 dopamine receptor binding / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of synaptic transmission / response to mechanical stimulus / response to electrical stimulus / synaptic cleft / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / cellular response to forskolin / monoatomic cation channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / response to organonitrogen compound / ionotropic glutamate receptor binding / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / ionotropic glutamate receptor signaling pathway / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to cocaine / synaptic membrane / synaptic transmission, glutamatergic / learning / long-term synaptic potentiation / response to cytokine / hippocampus development / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / calcium channel activity / terminal bouton / response to organic cyclic compound / response to toxic substance / cerebral cortex development / memory
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Response regulator / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Response regulator / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HYY / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsRegan, M.C. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F32NS093753 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH085926 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural elements of a pH-sensitive inhibitor binding site in NMDA receptors
Authors: Regan, M.C. / Furukawa, H.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_angle / 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_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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2B
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,51126
Polymers168,8864
Non-polymers3,62522
Water5,711317
1
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,72914
Polymers84,4432
Non-polymers2,28612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,78212
Polymers84,4432
Non-polymers1,33910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)268.594, 59.835, 146.015
Angle α, β, γ (deg.)90.000, 116.860, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLYGLYAA23 - 4051 - 383
21ASPASPGLYGLYCC23 - 4051 - 383
12PROPROARGARGBB32 - 3931 - 362
22PROPROARGARGDD32 - 3931 - 362

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.934312, -0.356451, -0.001687), (-0.354162, 0.928827, -0.108855), (0.040369, -0.101107, -0.994056)17.642281, 6.47911, 58.159328
3given(1), (1), (1)
4given(-0.93496, -0.354051, -0.022315), (-0.349931, 0.93076, -0.10599), (0.058296, -0.091288, -0.994117)18.6071, 6.59622, 59.111012

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 4 molecules ACBD

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 43162.270 Da / Num. of mol.: 2 / Fragment: Extracellular residues 23-407 / Mutation: N61Q, N371Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A1L8F5J9
#2: Protein Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B


Mass: 41280.820 Da / Num. of mol.: 2 / Fragment: Extracellular residues 32-394 / Mutation: N348D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00960

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Sugars , 2 types, 7 molecules

#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.: 1
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: 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.: 6
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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Non-polymers , 4 types, 332 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-HYY / N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide


Mass: 475.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28Cl2N2O4S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.91 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 83106 / % possible obs: 91 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.054 / Rrim(I) all: 0.107 / Χ2: 0.923 / Net I/σ(I): 7.7 / Num. measured all: 299032
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.31-2.351.90.60621500.6570.4670.770.91548.1
2.35-2.3920.60125310.6150.4530.7570.91655.2
2.39-2.442.20.6329220.6830.4570.7840.96965.3
2.44-2.492.40.57734370.7210.4080.7110.89475.3
2.49-2.542.70.62439420.690.4280.7610.92287.1
2.54-2.630.66243870.6610.4320.7950.92496.4
2.6-2.673.50.6344410.7510.3850.7410.92899
2.67-2.743.70.54945260.80.3240.640.94499.1
2.74-2.823.60.42845150.8210.260.5030.94999.3
2.82-2.913.80.37344880.8980.2160.4330.98799.2
2.91-3.013.80.28345060.9250.1650.3290.99299.3
3.01-3.134.20.22445630.9620.1210.2551.00499.4
3.13-3.284.30.16145150.9790.0860.1830.99199.5
3.28-3.454.20.11945600.9860.0640.1350.97899.6
3.45-3.674.20.08745440.9910.0480.10.9699.6
3.67-3.954.10.06645800.9940.0360.0750.92999.5
3.95-4.354.10.05245260.9950.0290.060.89399.3
4.35-4.983.80.04345980.9960.0250.050.8299.4
4.98-6.273.50.04246120.9950.0260.050.77499.5
6.27-504.30.03747630.9960.020.0420.76199.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QEL

3qel


Resolution: 2.31→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.019 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351 / ESU R Free: 0.235
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3520 5 %RANDOM
Rwork0.1937 ---
obs0.1953 67430 77.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 146.95 Å2 / Biso mean: 42.339 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å21 Å2
2---2.43 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 2.31→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10701 0 232 317 11250
Biso mean--74.62 33.98 -
Num. residues----1420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01911172
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210309
X-RAY DIFFRACTIONr_angle_refined_deg0.3631.97315269
X-RAY DIFFRACTIONr_angle_other_deg0.41323593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.96551410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1724.384438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.479151659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3631546
X-RAY DIFFRACTIONr_chiral_restr0.0350.21808
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02112611
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022473
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A30463.62
2B29624.18
LS refinement shellResolution: 2.311→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 81 -
Rwork0.255 1282 -
all-1363 -
obs--20.61 %
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)
11.2363-0.50280.75711.4263-0.69863.026-0.15810.140.1389-0.0001-0.01170.0284-0.13320.12770.16990.0334-0.0489-0.02380.239-0.02020.037853.7172-63.749711.4215
22.56551.12050.28022.28830.1022.2378-0.0833-0.23280.09790.3316-0.04190.1621-0.2695-0.13740.12520.22620.032-0.05480.2336-0.01810.051148.3574-56.10444.2626
31.54010.34011.04732.96870.94882.5194-0.0155-0.0845-0.02640.4945-0.04810.15520.0202-0.18360.06360.23830.0166-0.06070.24520.10440.1325-10.2285-72.777453.942
43.7317-0.560.60831.1481-0.22611.2921-0.03270.36210.0145-0.14410.0556-0.1127-0.04230.2112-0.02290.1507-0.0111-0.07430.398-0.02920.0788-6.8553-67.544420.8972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 507
2X-RAY DIFFRACTION2B32 - 502
3X-RAY DIFFRACTION3C23 - 502
4X-RAY DIFFRACTION4D32 - 502

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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