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- PDB-6gl4: Structure of GluA2o ligand-binding domain (S1S2J) in complex with... -

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Basic information

Entry
Database: PDB / ID: 6gl4
TitleStructure of GluA2o ligand-binding domain (S1S2J) in complex with glutamate and sodium bromide at 1.95 A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor / GluA2o ligand-binding domain / agonist
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / immunoglobulin binding / asymmetric synapse / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cytoskeletal protein binding / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / postsynaptic density membrane / modulation of chemical synaptic transmission / cerebral cortex development / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / synaptic vesicle / signaling receptor activity / presynapse / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / 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
ACETATE ION / BROMIDE ION / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.948 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: Neuron / Year: 2019
Title: Nanoscale Mobility of the Apo State and TARP Stoichiometry Dictate the Gating Behavior of Alternatively Spliced AMPA Receptors.
Authors: Dawe, G.B. / Kadir, M.F. / Venskutonyte, R. / Perozzo, A.M. / Yan, Y. / Alexander, R.P.D. / Navarrete, C. / Santander, E.A. / Arsenault, M. / Fuentes, C. / Aurousseau, M.R.P. / Frydenvang, K. ...Authors: Dawe, G.B. / Kadir, M.F. / Venskutonyte, R. / Perozzo, A.M. / Yan, Y. / Alexander, R.P.D. / Navarrete, C. / Santander, E.A. / Arsenault, M. / Fuentes, C. / Aurousseau, M.R.P. / Frydenvang, K. / Barrera, N.P. / Kastrup, J.S. / Edwardson, J.M. / Bowie, D.
History
DepositionMay 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,52814
Polymers58,5572
Non-polymers97112
Water7,584421
1
A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,51512
Polymers58,5572
Non-polymers95810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3490 Å2
ΔGint-6 kcal/mol
Surface area23590 Å2
MethodPISA
2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,54116
Polymers58,5572
Non-polymers98414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area3920 Å2
ΔGint-54 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.717, 47.715, 116.713
Angle α, β, γ (deg.)90.000, 93.790, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 24 or resid 26...
21(chain B and (resid 1 through 24 or resid 26...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU(chain A and (resid 1 through 24 or resid 26...AA1 - 241 - 24
12LEULEUGLUGLU(chain A and (resid 1 through 24 or resid 26...AA26 - 4226 - 42
13ALAALALEULEU(chain A and (resid 1 through 24 or resid 26...AA44 - 9444 - 94
14ARGARGILEILE(chain A and (resid 1 through 24 or resid 26...AA96 - 11596 - 115
15SERSERALAALA(chain A and (resid 1 through 24 or resid 26...AA142 - 165142 - 165
16ASNASNGLYGLY(chain A and (resid 1 through 24 or resid 26...AA197 - 231197 - 231
17ALAALASERSER(chain A and (resid 1 through 24 or resid 26...AA233 - 263233 - 263
21GLYGLYGLUGLU(chain B and (resid 1 through 24 or resid 26...BB1 - 241 - 24
22LEULEUGLUGLU(chain B and (resid 1 through 24 or resid 26...BB26 - 4226 - 42
23ALAALALEULEU(chain B and (resid 1 through 24 or resid 26...BB44 - 9444 - 94
24ARGARGILEILE(chain B and (resid 1 through 24 or resid 26...BB96 - 11596 - 115
25SERSERALAALA(chain B and (resid 1 through 24 or resid 26...BB142 - 165142 - 165
26ASNASNGLYGLY(chain B and (resid 1 through 24 or resid 26...BB197 - 231197 - 231
27ALAALASERSER(chain B and (resid 1 through 24 or resid 26...BB233 - 263233 - 263

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor 2,Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29278.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The ...Details: The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.,The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.,The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.,The protein crystallized is the extracellular ligand-binding domain of GluA2o. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B (DE3) / References: UniProt: P19491

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Non-polymers , 6 types, 433 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG4000, 0.2M sodium sulfate, 0.1M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91949 Å / Relative weight: 1
ReflectionResolution: 1.948→116.457 Å / Num. all: 37848 / Num. obs: 37848 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 19.88 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Rsym value: 0.089 / Net I/av σ(I): 7.8 / Net I/σ(I): 16.2 / Num. measured all: 286755
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.067.60.4681.64132254500.1820.5020.4684.4100
2.06-2.187.60.2972.63948852050.1150.3190.2976.6100
2.18-2.337.60.213.63709248800.0810.2250.218.9100
2.33-2.527.60.1734.43473845600.0670.1860.17310.4100
2.52-2.767.60.1216.33192541940.0470.130.12114.1100
2.76-3.087.60.0858.62901238050.0330.0910.08519.5100
3.08-3.567.60.05712.32563533710.0220.0610.05728.9100
3.56-4.367.60.04415.32174028710.0170.0480.04437.6100
4.36-6.177.50.04215.61673622360.0160.0450.04236100
6.17-46.6157.10.0414.9906712760.0160.0440.0435.299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å47.59 Å
Translation2.01 Å47.59 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TDJ

3tdj


Resolution: 1.948→46.615 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 1984 5.24 %
Rwork0.1628 35852 -
obs0.1648 37836 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.39 Å2 / Biso mean: 27.7342 Å2 / Biso min: 8.31 Å2
Refinement stepCycle: final / Resolution: 1.948→46.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 38 430 4558
Biso mean--29.67 31.51 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054271
X-RAY DIFFRACTIONf_angle_d0.7365752
X-RAY DIFFRACTIONf_chiral_restr0.048633
X-RAY DIFFRACTIONf_plane_restr0.004726
X-RAY DIFFRACTIONf_dihedral_angle_d9.7172606
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2958X-RAY DIFFRACTION4.589TORSIONAL
12B2958X-RAY DIFFRACTION4.589TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9481-1.99690.2636850.19612509259499
1.9969-2.05080.23991100.182125952705100
2.0508-2.11120.23581200.180225582678100
2.1112-2.17930.21771860.165925192705100
2.1793-2.25720.2241810.167424962677100
2.2572-2.34760.23691570.171625282685100
2.3476-2.45440.21571070.170725962703100
2.4544-2.58380.19631170.174325842701100
2.5838-2.74570.25831450.171125532698100
2.7457-2.95770.26091340.171825492683100
2.9577-3.25520.21791800.168225212701100
3.2552-3.72610.15111570.149125892746100
3.7261-4.69380.15431670.128125842751100
4.6938-46.62850.171380.171426712809100
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)
12.93030.3801-0.89322.0053-0.10042.82390.1534-0.08330.13470.2635-0.06840.0791-0.1032-0.0621-0.06710.18040.01140.03540.11720.00650.131334.569518.58820.0532
20.48340.63930.27572.84460.63090.41940.02470.0054-0.04810.05420.0364-0.15150.00960.0417-0.03190.15430.03040.01180.16580.00460.102350.285818.649314.5385
32.9924-0.4144-0.08843.27790.30342.229-0.07590.0075-0.04740.14980.1966-0.30460.18710.5439-0.07530.19470.0936-0.0120.297-0.02440.135762.12432.289517.1811
40.93720.82240.42691.94210.79440.9578-0.00980.04750.10990.03720.00320.1293-0.0941-0.1270.01140.2380.04090.03190.19160.03050.126342.573928.274210.2381
52.6808-0.19020.35853.0408-0.24972.6497-0.05210.1567-0.0075-0.24450.0557-0.1920.10410.25430.00890.1173-0.00260.04290.1549-0.0130.171682.682540.960741.7558
60.6178-0.1735-0.06052.2737-0.21510.6129-0.00150.0968-0.0179-0.2497-0.00930.06750.0546-0.0160.01440.1293-0.0089-0.00170.16770.00010.11766.569740.840943.2409
74.4189-1.1763-0.3455.2651-1.00253.5355-0.23440.49170.1932-0.46650.40040.42910.0204-0.3146-0.09270.1649-0.0965-0.07690.32360.07820.251753.925453.507440.5945
80.8563-0.10240.18682.0432-1.08631.401-0.06490.0850.0741-0.22330.14120.06260.0146-0.11-0.0550.1649-0.03640.02030.1756-0.02220.127467.636652.611644.4527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 123 )A48 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 187 )A124 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 263 )A188 - 263
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 47 )B1 - 47
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 123 )B48 - 123
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 152 )B124 - 152
8X-RAY DIFFRACTION8chain 'B' and (resid 153 through 263 )B153 - 263

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