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- PDB-7qtv: Beryllium fluoride form of the Na+,K+-ATPase (E2-BeFx) -

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Basic information

Entry
Database: PDB / ID: 7qtv
TitleBeryllium fluoride form of the Na+,K+-ATPase (E2-BeFx)
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • FXYD domain-containing ion transport regulator
KeywordsMEMBRANE PROTEIN / Pig kidney Na+ / K+-ATPase
Function / homology
Function and homology information


Basigin interactions / Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / Ion transport by P-type ATPases / positive regulation of potassium ion import across plasma membrane / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding ...Basigin interactions / Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / Ion transport by P-type ATPases / positive regulation of potassium ion import across plasma membrane / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / sodium channel regulator activity / regulation of sodium ion transport / proton transmembrane transport / sarcolemma / transmembrane transport / melanosome / protein-macromolecule adaptor activity / ATPase binding / basolateral plasma membrane / cell adhesion / apical plasma membrane / axon / innate immune response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. ...: / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Chem-1AT / Chem-1DS / BERYLLIUM TRIFLUORIDE ION / CHOLESTEROL / Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-1 / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.05 Å
AuthorsFruergaard, M.U. / Dach, I. / Andersen, J.L. / Ozol, M. / Shahsavar, A. / Quistgaard, E.M. / Poulsen, H. / Fedosova, N.U. / Nissen, P.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-7016-00125 Denmark
LundbeckfondenR155-2015-2666 Denmark
LundbeckfondenR310-2018-3713 Denmark
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The Na + ,K + -ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state.
Authors: Fruergaard, M.U. / Dach, I. / Andersen, J.L. / Ozol, M. / Shahsavar, A. / Quistgaard, E.M. / Poulsen, H. / Fedosova, N.U. / Nissen, P.
History
DepositionJan 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: FXYD domain-containing ion transport regulator
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,31925
Polymers310,1926
Non-polymers4,12719
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18830 Å2
ΔGint-106 kcal/mol
Surface area122440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.470, 118.080, 494.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 through 80 or resid 155 through 275))
21(chain C and (resid 21 through 80 or resid 155 through 275))
12(chain A and resid 377 through 588)
22(chain C and resid 377 through 588)
13(chain A and (resid 81 through 154 or resid 276...
23(chain C and (resid 81 through 154 or resid 276...
14(chain A and (resid 349 through 376 or resid 589 through 746))
24(chain C and (resid 349 through 376 or resid 589 through 746))
15(chain B and (resid 63 through 90 or resid 92 through 303))
25(chain D and (resid 63 through 90 or resid 92 through 303))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSPROPRO(chain A and (resid 21 through 80 or resid 155 through 275))AA21 - 8026 - 85
121LYSLYSTHRTHR(chain A and (resid 21 through 80 or resid 155 through 275))AA155 - 275160 - 280
211LYSLYSPROPRO(chain C and (resid 21 through 80 or resid 155 through 275))CD21 - 8026 - 85
221LYSLYSTHRTHR(chain C and (resid 21 through 80 or resid 155 through 275))CD155 - 275160 - 280
112ASNASNPROPRO(chain A and resid 377 through 588)AA377 - 588382 - 593
212ASNASNPROPRO(chain C and resid 377 through 588)CD377 - 588382 - 593
113GLUGLUPHEPHE(chain A and (resid 81 through 154 or resid 276...AA81 - 15486 - 159
123PROPROASNASN(chain A and (resid 81 through 154 or resid 276...AA276 - 348281 - 353
133ASNASNTYRTYR(chain A and (resid 81 through 154 or resid 276...AA747 - 1016752 - 1021
213GLUGLUPHEPHE(chain C and (resid 81 through 154 or resid 276...CD81 - 15486 - 159
223PROPROASNASN(chain C and (resid 81 through 154 or resid 276...CD276 - 348281 - 353
233ASNASNTYRTYR(chain C and (resid 81 through 154 or resid 276...CD747 - 1016752 - 1021
114CYSCYSGLNGLN(chain A and (resid 349 through 376 or resid 589 through 746))AA349 - 376354 - 381
124ARGARGASPASP(chain A and (resid 349 through 376 or resid 589 through 746))AA589 - 746594 - 751
214CYSCYSGLNGLN(chain C and (resid 349 through 376 or resid 589 through 746))CD349 - 376354 - 381
224ARGARGASPASP(chain C and (resid 349 through 376 or resid 589 through 746))CD589 - 746594 - 751
115GLUGLUPHEPHE(chain B and (resid 63 through 90 or resid 92 through 303))BB63 - 9063 - 90
125PROPROSERSER(chain B and (resid 63 through 90 or resid 92 through 303))BB92 - 30392 - 303
215GLUGLUPHEPHE(chain D and (resid 63 through 90 or resid 92 through 303))DE63 - 9063 - 90
225PROPROSERSER(chain D and (resid 63 through 90 or resid 92 through 303))DE92 - 30392 - 303

NCS ensembles :
ID
1
2
3
4
5

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Components

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Sodium/potassium-transporting ATPase subunit ... , 2 types, 4 molecules ACBD

#1: Protein Sodium/potassium-transporting ATPase subunit alpha-1 / Na(+)/K(+) ATPase alpha-1 subunit / Sodium pump subunit alpha-1


Mass: 112797.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP1A1 / Production host: Sus scrofa (pig) / References: UniProt: P05024, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35204.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP1B1 / Production host: Sus scrofa (pig) / References: UniProt: P05027

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Protein , 1 types, 2 molecules GE

#3: Protein FXYD domain-containing ion transport regulator


Mass: 7094.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: FXYD2 / Production host: Sus scrofa (pig) / References: UniProt: Q58K79

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Sugars , 2 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#10: 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.: 4 / Source method: obtained synthetically / 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 , 6 types, 23 molecules

#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-1AT / beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside


Mass: 496.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H40O12
#7: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#8: Chemical ChemComp-1DS / 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside


Mass: 496.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H40O12
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 5.53 Å3/Da / Density % sol: 77.76 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Protein sample was mixed in a 1:1 ratio with reservoir solution containing 16.5 % (wt/vol) polyethylene glycol 2000 monomethyl ether (PEG 2000 MME), 10 % (vol/vol) glycerol, 175 mM MgCl2, ...Details: Protein sample was mixed in a 1:1 ratio with reservoir solution containing 16.5 % (wt/vol) polyethylene glycol 2000 monomethyl ether (PEG 2000 MME), 10 % (vol/vol) glycerol, 175 mM MgCl2, 150 mM NaCl, 20 mM HEPES/MES pH 6.2 and 2 mM DTT. The crystals were dehydrated overnight at 4C against a 30 % PEG 2000 MME reservoir solution before flash-cooling.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)11
SYNCHROTRONSLS X06DA21
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELOct 29, 2015
DECTRIS PILATUS 2M2PIXELDec 6, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 4.05→29.67 Å / Num. obs: 57347 / % possible obs: 99.5 % / Redundancy: 26.2 % / Biso Wilson estimate: 147.73 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.4
Reflection shellResolution: 4.05→4.2 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4625 / CC1/2: 0.263 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7d91

7d91


Resolution: 4.05→29.67 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.94 / Stereochemistry target values: ML
Details: The data has been anisotropically truncated to 4.0 A resolution
RfactorNum. reflection% reflection
Rfree0.2811 1928 4.92 %
Rwork0.2465 37220 -
obs0.2483 39148 68.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 510.79 Å2 / Biso mean: 188.1761 Å2 / Biso min: 65.47 Å2
Refinement stepCycle: final / Resolution: 4.05→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20734 0 274 9 21017
Biso mean--175.64 157.81 -
Num. residues----2638
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1100X-RAY DIFFRACTION8.043TORSIONAL
12C1100X-RAY DIFFRACTION8.043TORSIONAL
21A1286X-RAY DIFFRACTION8.043TORSIONAL
22C1286X-RAY DIFFRACTION8.043TORSIONAL
31A2984X-RAY DIFFRACTION8.043TORSIONAL
32C2984X-RAY DIFFRACTION8.043TORSIONAL
41A1116X-RAY DIFFRACTION8.043TORSIONAL
42C1116X-RAY DIFFRACTION8.043TORSIONAL
51B1454X-RAY DIFFRACTION8.043TORSIONAL
52D1454X-RAY DIFFRACTION8.043TORSIONAL
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 (%)
4.05-4.150.295670.38951471544
4.15-4.270.3021140.330445947312
4.27-4.390.3583330.310986089322
4.39-4.530.333760.28831480155639
4.53-4.690.32331080.28071988209652
4.69-4.880.30841150.26812483259864
4.88-5.10.29481700.27162890306076
5.1-5.370.33221540.26163447360189
5.37-5.70.33781960.288337913987100
5.7-6.140.29662180.296338704088100
6.14-6.750.30792130.279538424055100
6.75-7.710.27371950.232639124107100
7.71-9.660.24821980.199439624160100
9.66-29.670.24892310.224140894320100
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)
14.0926-0.31260.42272.52920.38253.7159-0.06210.07470.84270.03470.261-0.0496-0.9793-0.332-0.49630.80170.13540.29951.24850.01760.9139-5.7742-18.5987-9.409
21.14750.5009-0.55423.6568-0.10165.9892-0.5173-0.1127-0.80330.4192-0.5084-0.30251.13630.77550.81331.6056-0.14670.33951.35260.06461.367344.4381-106.1295-114.8282
30.33080.39650.20213.99080.95425.39130.2015-0.43870.0190.3824-0.0318-0.1657-0.18860.2715-0.32930.55410.03980.12291.06470.00030.917321.0267-26.7816-14.2376
43.45440.2283-2.05092.9491-0.14163.98620.2687-0.1421-0.443-1.230.0318-0.1475-0.43470.6298-0.09991.55960.30710.23240.7213-0.16391.049453.4978-79.9835-108.1642
53.20191.1183-2.00935.0493-0.06522.47440.8964-1.8824-1.18182.18480.0722-0.04480.6403-0.0543-0.36451.4852-0.09650.15242.7610.85451.60673.9202-50.26138.8453
63.812-1.4652.75092.5925-0.09682.1337-0.12212.8177-0.546-1.7639-0.51612.4725-0.20920.30240.15532.88390.1926-0.91992.7865-0.35841.959426.1849-78.7046-133.3989
71.0472-0.71370.31920.9261-0.49833.0098-0.11350.0260.3847-0.15790.13710.0434-0.25260.01740.05750.6018-0.03870.26990.78850.00790.91630.7324-31.8721-59.1004
80.67690.42571.151.42080.93283.95150.14060.1427-0.40440.2016-0.1363-0.34131.17470.6197-0.12781.35520.16420.34480.74460.0591.091651.588-71.2871-62.8455
92.2991-2.67852.27273.4008-1.56885.32790.88792.15940.8552-1.4557-0.7973-0.13960.05590.07960.04461.7687-0.01240.39291.94480.47871.33831.1321-29.1785-106.6443
100.6518-1.4353-0.84686.0240.30654.45270.0673-0.2522-0.04290.55160.0288-0.65261.30740.4451-0.0171.7539-0.0189-0.19561.47370.1231.236751.2547-74.6858-15.4448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 21:80 or resseq 155:275)A21 - 80
2X-RAY DIFFRACTION1chain A and (resseq 21:80 or resseq 155:275)A155 - 275
3X-RAY DIFFRACTION2chain C and (resseq 21:80 or resseq 155:275)C21 - 80
4X-RAY DIFFRACTION2chain C and (resseq 21:80 or resseq 155:275)C155 - 275
5X-RAY DIFFRACTION3chain A and (resseq 349:376 or resseq 589:746)A349 - 376
6X-RAY DIFFRACTION3chain A and (resseq 349:376 or resseq 589:746)A589 - 746
7X-RAY DIFFRACTION4chain C and (resseq 349:376 or resseq 589:746)C349 - 376
8X-RAY DIFFRACTION4chain C and (resseq 349:376 or resseq 589:746)C589 - 746
9X-RAY DIFFRACTION5chain A and (resseq 377:588)A377 - 588
10X-RAY DIFFRACTION6chain C and (resseq 377:588)C377 - 588
11X-RAY DIFFRACTION7chain A and (resseq 81:154 or resseq 276:348 or resseq 747:1016) or chain B and resseq 16:62 or chain GA81 - 154
12X-RAY DIFFRACTION7chain A and (resseq 81:154 or resseq 276:348 or resseq 747:1016) or chain B and resseq 16:62 or chain GA276 - 348
13X-RAY DIFFRACTION7chain A and (resseq 81:154 or resseq 276:348 or resseq 747:1016) or chain B and resseq 16:62 or chain GA747 - 1016
14X-RAY DIFFRACTION8chain C and (resseq 81:154 or resseq 276:348 or resseq 747:1016) or chain D and resseq 19:62 or chain EC81 - 154
15X-RAY DIFFRACTION8chain C and (resseq 81:154 or resseq 276:348 or resseq 747:1016) or chain D and resseq 19:62 or chain EC276 - 348
16X-RAY DIFFRACTION8chain C and (resseq 81:154 or resseq 276:348 or resseq 747:1016) or chain D and resseq 19:62 or chain EC747 - 1016
17X-RAY DIFFRACTION9chain B and (resseq 63:303)B63 - 303
18X-RAY DIFFRACTION10chain D and (resseq 63:303)D63 - 303

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