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- PDB-3u94: Crystal structure of the GluK3 ligand binding domain complex with... -

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Basic information

Entry
Database: PDB / ID: 3u94
TitleCrystal structure of the GluK3 ligand binding domain complex with glutamate and zinc: P21212 form
ComponentsGlutamate receptor, ionotropic kainate 3
KeywordsMEMBRANE PROTEIN / ION CHANNEL
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / dendrite / glutamatergic synapse / 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
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.962 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: Neuron / Year: 2012
Title: Zinc Potentiates GluK3 Glutamate Receptor Function by Stabilizing the Ligand Binding Domain Dimer Interface.
Authors: Veran, J. / Kumar, J. / Pinheiro, P.S. / Athane, A. / Mayer, M.L. / Perrais, D. / Mulle, C.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: 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_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 3
B: Glutamate receptor, ionotropic kainate 3
C: Glutamate receptor, ionotropic kainate 3
D: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,88024
Polymers116,2134
Non-polymers1,66620
Water12,376687
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3975
Polymers29,0531
Non-polymers3434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4275
Polymers29,0531
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5587
Polymers29,0531
Non-polymers5056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4987
Polymers29,0531
Non-polymers4446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.155, 111.374, 129.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-80-

HIS

DetailsTHE OBSERVED BIOLOGICAL UNIT DOES NOT OCCUR FOR THE FULL LENGTH PROTEIN THEREFORE, IS NOT BIOLOGICALLY RELEVANT

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutamate receptor, ionotropic kainate 3


Mass: 29053.371 Da / Num. of mol.: 4 / Fragment: unp residues 433-546 and 669-807
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK3 / Plasmid: PET22 modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) / References: UniProt: P42264

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Non-polymers , 5 types, 707 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS ...THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (433-546 AND 669-807)

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6% PEG 3350, 0.1 M BisTrisPropane, 0.2 M NaSulfate, 5 mM glutamate, 10 mM ZnAcate,, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 19, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→40 Å / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.9
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.7 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S50

1s50


Resolution: 1.962→38.937 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 4529 4.99 %RANDOM
Rwork0.1934 ---
obs0.196 92846 97.59 %-
all-92846 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.242 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9585 Å2-0 Å20 Å2
2--4.6297 Å2-0 Å2
3----9.5881 Å2
Refinement stepCycle: LAST / Resolution: 1.962→38.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8056 0 64 687 8807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178297
X-RAY DIFFRACTIONf_angle_d1.38411163
X-RAY DIFFRACTIONf_dihedral_angle_d14.2793111
X-RAY DIFFRACTIONf_chiral_restr0.0811230
X-RAY DIFFRACTIONf_plane_restr0.0071399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.962-1.98430.27641430.21362613X-RAY DIFFRACTION90
1.9843-2.00770.27391440.20772830X-RAY DIFFRACTION98
2.0077-2.03220.27111470.20652846X-RAY DIFFRACTION98
2.0322-2.05790.2581550.19462839X-RAY DIFFRACTION98
2.0579-2.0850.22531410.19732843X-RAY DIFFRACTION98
2.085-2.11350.27021370.19542864X-RAY DIFFRACTION98
2.1135-2.14370.25441550.19362861X-RAY DIFFRACTION97
2.1437-2.17570.27841440.18582838X-RAY DIFFRACTION98
2.1757-2.20970.24721580.1912835X-RAY DIFFRACTION98
2.2097-2.24590.25371490.18912864X-RAY DIFFRACTION98
2.2459-2.28460.25211480.17942854X-RAY DIFFRACTION97
2.2846-2.32620.22531350.18392835X-RAY DIFFRACTION97
2.3262-2.37090.26851380.20052871X-RAY DIFFRACTION97
2.3709-2.41930.26951470.20822865X-RAY DIFFRACTION98
2.4193-2.47190.28731470.21072855X-RAY DIFFRACTION97
2.4719-2.52940.2841490.21122826X-RAY DIFFRACTION97
2.5294-2.59260.27281660.20272818X-RAY DIFFRACTION97
2.5926-2.66270.28431540.20062829X-RAY DIFFRACTION97
2.6627-2.74110.27421350.20872850X-RAY DIFFRACTION97
2.7411-2.82950.26471690.21122830X-RAY DIFFRACTION97
2.8295-2.93060.27681560.21112828X-RAY DIFFRACTION96
2.9306-3.04790.30741740.2082866X-RAY DIFFRACTION98
3.0479-3.18650.23791540.20722933X-RAY DIFFRACTION99
3.1865-3.35450.21991600.20252924X-RAY DIFFRACTION100
3.3545-3.56450.26041670.19912961X-RAY DIFFRACTION99
3.5645-3.83950.22491400.1892956X-RAY DIFFRACTION99
3.8395-4.22550.1781520.1662974X-RAY DIFFRACTION100
4.2255-4.83590.15731440.14083010X-RAY DIFFRACTION99
4.8359-6.0890.25951560.18663029X-RAY DIFFRACTION100
6.089-38.94510.29331650.21963108X-RAY DIFFRACTION97
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)
11.991-0.4097-0.18530.8053-0.67471.5590.0109-0.459-0.3680.6773-0.00210.01340.24180.03740.01570.52-0.099-0.0560.2360.09890.21738.77667.4722116.5718
23.09411.06960.41432.0486-0.27091.38740.0659-0.0076-0.51910.2571-0.0302-0.40110.1870.19140.02640.2751-0.0334-0.06910.2012-0.00570.244115.16249.7211105.8857
31.8089-0.1124-0.10812.30.09341.69530.00390.0275-0.15540.195-0.0159-0.23930.02980.197-0.01870.2071-0.0509-0.07080.1530.00470.196714.692614.8672100.9007
40.70540.12890.17060.45860.12640.7985-0.0666-0.1440.14520.2734-0.0151-0.2012-0.39060.3168-0.1770.5085-0.2463-0.33020.2235-0.02470.084522.336231.0472114.6202
52.3246-0.3144-0.22331.57360.24031.97790.0636-0.1046-0.03340.2234-0.07010.032-0.0084-0.0943-0.02780.2161-0.0735-0.01620.1445-0.0150.17851.196815.7225102.2912
61.77540.53030.83050.33190.49670.74420.0275-0.69720.35180.7389-0.40090.1302-0.3038-0.25380.13910.6052-0.046-0.03560.4613-0.05780.16762.925124.8724123.0328
72.2746-0.0006-0.05451.1893-0.55890.8165-0.0343-0.45940.52590.40540.06680.0174-0.65890.1084-0.18640.7641-0.11520.06420.2621-0.19340.2727-8.870748.6323114.3586
81.4039-0.0933-0.50191.71330.17451.244-0.0018-0.00090.35670.27360.13650.3089-0.5412-0.3357-0.01330.46740.0970.12930.16320.00210.3328-21.719742.5872102.1563
91.14360.4272-0.19080.7192-0.31.2938-0.112-0.0599-0.02390.19920.06560.18940.1627-0.2931-0.14940.40710.02020.19480.1985-0.02910.201-23.889823.954109.1543
100.41290.1766-0.42560.4921-0.07621.32310.0147-0.21230.05680.4107-0.01790.231-0.1116-0.1979-0.07670.48890.06980.21330.2675-0.03720.1689-21.597727.5331117.114
112.2685-0.22060.10731.5286-0.47421.9028-0.0318-0.11170.20340.1993-0.0367-0.031-0.40710.3445-0.04350.4621-0.14770.0030.2411-0.00740.1687-2.397240.1999102.3387
121.7969-0.00440.2316-0.0001-0.00050.030.0572-0.6809-0.11990.8325-0.16960.15060.07020.00820.07920.6478-0.03960.07540.4598-0.04510.1638-5.359230.9957123.0007
131.84170.2668-0.37181.3041-0.33382.15490.05320.48210.0263-0.17940.09890.1118-0.22270.0447-0.07250.1428-0.03030.01060.31750.00360.1762-12.661919.662968.9269
141.11370.05070.14830.9037-0.12521.08020.0360.1013-0.26710.06830.09410.1880.0852-0.22590.01640.0929-0.045-0.00390.19840.00660.2191-19.154810.511681.4242
151.67240.6419-0.52471.4299-0.84631.34120.0436-0.0646-0.46-0.05310.2010.21420.3414-0.4890.14070.1988-0.1896-0.05720.38130.12790.3631-31.89153.202783.2076
161.9381-0.10490.26850.7091-0.23130.89250.025-0.03590.0014-0.02140.12650.2161-0.0335-0.3829-0.08920.11080.00610.00510.29210.03250.1799-27.197816.016382.3372
172.5104-2.21850.31763.8274-0.67341.51610.1783-0.11760.1260.1262-0.02550.0045-0.25510.1011-0.07340.1621-0.06230.03580.1512-0.0250.1591-7.733522.757689.46
186.5852.0046-3.00394.1861.68037.59040.24950.27760.82420.03620.03140.6431-0.8228-0.8031-0.140.2340.09940.04190.19960.01060.2336-20.648629.137481.2314
191.3954-0.10710.1931.93720.22922.75950.10840.42550.1383-0.132-0.0286-0.04570.15420.1182-0.02550.2195-0.0190.00650.25230.04670.186211.990536.088469.2449
201.17240.04140.16721.0951-0.11321.52360.14120.11670.49880.028-0.0042-0.1243-0.29990.11770.01820.229-0.0860.03750.17260.04450.323711.463445.935580.3763
211.86620.15220.36471.5660.26020.86610.1289-0.07850.36120.1102-0.0135-0.3466-0.33870.69970.08980.3275-0.26110.00440.5115-0.02350.401136.480948.083686.4465
221.7884-0.0548-0.32190.96330.04741.03950.0509-0.09810.0568-0.1149-0.0389-0.171-0.15210.66320.04210.2248-0.0694-0.01810.4090.01120.243430.936538.576281.4125
231.7413-0.4979-0.26853.3502-1.61331.85430.1526-0.19420.17950.3229-0.03050.053-0.4076-0.1312-0.07620.2899-0.10580.00330.23840.01350.21493.309342.196188.0309
243.10822.3617-1.65292.894-2.03846.94590.012-0.1168-0.3264-0.0258-0.0902-0.09980.15560.12810.09320.26-0.0515-0.08520.16750.03630.243414.343926.916785.8159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:40)
2X-RAY DIFFRACTION2(chain A and resid 41:72)
3X-RAY DIFFRACTION3(chain A and resid 73:106)
4X-RAY DIFFRACTION4(chain A and resid 107:216)
5X-RAY DIFFRACTION5(chain A and resid 217:246)
6X-RAY DIFFRACTION6(chain A and resid 247:257)
7X-RAY DIFFRACTION7(chain B and resid 4:53)
8X-RAY DIFFRACTION8(chain B and resid 54:97)
9X-RAY DIFFRACTION9(chain B and resid 98:159)
10X-RAY DIFFRACTION10(chain B and resid 160:216)
11X-RAY DIFFRACTION11(chain B and resid 217:246)
12X-RAY DIFFRACTION12(chain B and resid 247:256)
13X-RAY DIFFRACTION13(chain C and resid 4:31)
14X-RAY DIFFRACTION14(chain C and resid 32:134)
15X-RAY DIFFRACTION15(chain C and resid 135:173)
16X-RAY DIFFRACTION16(chain C and resid 174:225)
17X-RAY DIFFRACTION17(chain C and resid 226:246)
18X-RAY DIFFRACTION18(chain C and resid 247:251)
19X-RAY DIFFRACTION19(chain D and resid 4:31)
20X-RAY DIFFRACTION20(chain D and resid 32:108)
21X-RAY DIFFRACTION21(chain D and resid 109:166)
22X-RAY DIFFRACTION22(chain D and resid 167:216)
23X-RAY DIFFRACTION23(chain D and resid 217:237)
24X-RAY DIFFRACTION24(chain D and resid 238:251)

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