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- PDB-7agv: High-resolution structure of the K+/H+ antiporter subunit KhtT in... -

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Basic information

Entry
Database: PDB / ID: 7agv
TitleHigh-resolution structure of the K+/H+ antiporter subunit KhtT in complex with c-di-AMP
ComponentsK(+)/H(+) antiporter subunit KhtT
KeywordsTRANSPORT PROTEIN / Regulatory protein of K+/H+ antiporter / c-di-AMP binding protein
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / plasma membrane
Similarity search - Function
Potassium/proton antiporter subunit KhtT / : / K(+)/H(+) antiporter subunit KhtT, N-terminal domain / : / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Alpha-Beta Plaits ...Potassium/proton antiporter subunit KhtT / : / K(+)/H(+) antiporter subunit KhtT, N-terminal domain / : / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / ACETATE ION / K(+)/H(+) antiporter subunit KhtT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsCereija, T.B. / Guerra, J.P. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-029863(PTDC/BIA-BQM/29863/2017) Portugal
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: c-di-AMP, a likely master regulator of bacterial K + homeostasis machinery, activates a K + exporter.
Authors: Cereija, T.B. / Guerra, J.P.L. / Jorge, J.M.P. / Morais-Cabral, J.H.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 14, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K(+)/H(+) antiporter subunit KhtT
B: K(+)/H(+) antiporter subunit KhtT
C: K(+)/H(+) antiporter subunit KhtT
D: K(+)/H(+) antiporter subunit KhtT
E: K(+)/H(+) antiporter subunit KhtT
F: K(+)/H(+) antiporter subunit KhtT
G: K(+)/H(+) antiporter subunit KhtT
H: K(+)/H(+) antiporter subunit KhtT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,93826
Polymers151,5168
Non-polymers3,42218
Water8,647480
1
A: K(+)/H(+) antiporter subunit KhtT
B: K(+)/H(+) antiporter subunit KhtT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7557
Polymers37,8792
Non-polymers8765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: K(+)/H(+) antiporter subunit KhtT
D: K(+)/H(+) antiporter subunit KhtT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7146
Polymers37,8792
Non-polymers8364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: K(+)/H(+) antiporter subunit KhtT
F: K(+)/H(+) antiporter subunit KhtT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7146
Polymers37,8792
Non-polymers8364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: K(+)/H(+) antiporter subunit KhtT
H: K(+)/H(+) antiporter subunit KhtT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7557
Polymers37,8792
Non-polymers8765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.945, 127.598, 81.881
Angle α, β, γ (deg.)90.000, 95.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
K(+)/H(+) antiporter subunit KhtT


Mass: 18939.465 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: khtT, yhaT, BSU09860 / Production host: Escherichia coli (E. coli) / References: UniProt: O07535
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Sodium acetate pH 4.6 260 mM Calcium chloride 15% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→127.6 Å / Num. obs: 124845 / % possible obs: 98.5 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.023 / Rrim(I) all: 0.041 / Net I/σ(I): 14.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6197 / CC1/2: 0.514 / Rpim(I) all: 0.595 / Rrim(I) all: 1.045 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: SAD structure from data collected at SOLEIL-PROXIMA1.

Resolution: 1.85→81.462 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 6261 5.02 %
Rwork0.2042 118451 -
obs0.2062 124712 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.26 Å2 / Biso mean: 65.5735 Å2 / Biso min: 20.92 Å2
Refinement stepCycle: final / Resolution: 1.85→81.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10285 0 182 480 10947
Biso mean--50.46 54.46 -
Num. residues----1288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910984
X-RAY DIFFRACTIONf_angle_d1.18714833
X-RAY DIFFRACTIONf_chiral_restr0.0831645
X-RAY DIFFRACTIONf_plane_restr0.0041910
X-RAY DIFFRACTIONf_dihedral_angle_d14.5324271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.8710.3682190.3196395499
1.871-1.8930.31042220.2955395299
1.893-1.91610.29962130.2792398899
1.9161-1.94040.30161920.2665391599
1.9404-1.96590.29142260.251400099
1.9659-1.99290.27572300.2494392399
1.9929-2.02130.28272070.2552399599
2.0213-2.05150.28961940.2517397499
2.0515-2.08360.28412210.2452395099
2.0836-2.11770.30312080.2453392399
2.1177-2.15420.2791900.235403399
2.1542-2.19340.29622000.24396899
2.1934-2.23560.28131850.2335397899
2.2356-2.28120.27862190.2224398399
2.2812-2.33080.28661930.2286396099
2.3308-2.38510.26992010.2273392598
2.3851-2.44470.25632050.211398999
2.4447-2.51080.26842200.2216392598
2.5108-2.58470.26831990.222394598
2.5847-2.66810.27141990.2132396699
2.6681-2.76350.24662380.2121393399
2.7635-2.87420.25642260.2191392798
2.8742-3.0050.27851990.2227394398
3.005-3.16340.24772080.2108395498
3.1634-3.36160.26762170.212391498
3.3616-3.62120.22292040.1925391198
3.6212-3.98560.21011990.1782394397
3.9856-4.56220.18542320.1606389097
4.5622-5.74770.22151850.1758393697
5.7477-81.4620.2352100.2113385494
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)
18.92942.49720.48147.6043.31788.33720.0397-0.1925-0.0887-0.01510.1631-0.7177-0.16830.1987-0.1160.1307-0.01390.00880.19370.02110.294167.614873.77950.5867
23.3337-0.2016-0.48465.3299-2.50047.0660.08880.0762-0.1305-0.0643-0.02550.1609-0.1337-0.04760.08760.1403-0.0206-0.0050.2283-0.03680.260758.19877.9552-3.9736
30.7852-0.358-0.30613.0285-3.46456.84470.61491.08231.0494-0.1685-1.2876-0.8755-0.64070.59490.33130.6331-0.02980.13690.85190.10080.515773.650987.032-15.9222
46.3511.9746-1.58149.480.38836.53920.4483-0.1620.5961-0.8394-0.29210.0927-1.5648-0.1819-0.29651.01230.20190.16850.82590.05150.486669.845790.685-30.9084
57.58311.1174-0.32077.52320.49788.452-0.15150.3733-0.3934-0.72650.21831.5360.3904-0.9686-0.04590.29080.0111-0.12330.36940.01640.529949.087386.1499-8.1721
67.1804-0.1557-3.55467.5642-0.73788.9167-0.143-0.2480.370.93670.62141.2924-0.0363-0.6478-0.42030.36640.1440.03530.32920.07390.430152.644886.42650.7086
76.09440.26780.77287.18791.09833.2229-0.08490.5123-0.2814-0.61790.161-0.23880.29630.3068-0.14550.28540.01380.05270.2817-0.0380.165465.613774.7321-10.5974
87.3408-2.4833-8.02847.23332.35998.66860.2751.188-1.3073-1.0909-1.19140.44070.5353-0.62310.92720.90810.222-0.09880.8317-0.17590.512665.706666.3114-26.8411
97.20990.2232-4.02548.723-2.1377.1522-0.50850.2138-0.3584-0.6229-0.0465-0.61211.1261-0.20180.46970.87960.14050.10190.7925-0.00530.383270.262268.4304-29.8262
107.8039-0.1606-0.1212.25380.09076.7160.11520.51570.2824-0.61-0.02850.3638-0.3721-0.0796-0.01370.21730.0005-0.0250.1914-0.05310.323742.533644.4802-1.4569
116.43172.2822-1.7548.97450.79485.9177-0.05310.8184-0.1674-1.23680.4323-0.50820.12340.1041-0.1770.2430.0040.03970.264-0.05870.419351.885342.7575-4.1441
124.31951.05671.07666.19441.33673.77290.1639-0.4732-0.07610.3874-0.0143-0.1403-0.05820.1799-0.15620.2793-0.0815-0.06710.23920.0280.257452.757252.651413.765
138.7151-0.92740.29335.97852.53969.0990.3835-0.78820.2060.3826-0.71160.7473-0.6317-1.19480.37920.4278-0.05590.10520.3901-0.0550.364139.464158.420317.744
141.0580.2794-0.58051.55510.04315.1470.3051-0.68780.56821.7983-0.14520.0069-0.9914-0.69120.38441.7783-0.51740.43180.8379-0.3488-0.067838.094961.289435.4297
151.1682-2.6018-0.94225.83052.33837.14860.0903-0.71730.24121.0737-0.1707-1.5433-0.57461.0531-0.15480.9851-0.3605-0.13350.8607-0.0140.612549.269957.966231.1581
169.2721-2.7266-2.19589.3188-1.15976.65661.50110.73641.33321.75470.26251.9058-2.4695-1.5175-0.68341.09990.12830.47190.85410.01490.758934.466762.447325.3183
174.6401-0.363-0.47165.5245-1.81455.55960.23980.0945-0.57690.0754-0.1404-1.95410.76510.7914-0.06240.35620.0383-0.16540.320.00830.685162.302753.84137.8233
186.05320.14480.1426.7337-0.0647.95580.01060.6539-0.166-0.78010.0772-1.08750.11290.7521-0.09240.2553-0.03820.03170.3406-0.00630.478358.60654.8258-1.1186
193.75250.7414-1.548.4922-0.88315.7842-0.1663-0.01220.18490.1430.2365-0.45690.0689-0.3661-0.01840.2191-0.0146-0.03230.2515-0.01220.253244.724752.5847.0919
206.6064-4.06053.4435.0098-4.82084.7080.2203-1.0269-0.59681.34110.05350.72420.3648-0.4106-0.05890.4485-0.0762-0.00030.35570.04830.42844.010636.622312.9714
218.29384.0881-4.04657.7972-1.74067.95280.2978-1.6116-0.86551.0704-0.7125-0.9576-0.02930.4030.26680.57210.0053-0.11170.47580.12540.386249.266239.430822.4953
225.1434-1.3102-2.75344.9696-2.36073.34490.2717-0.7165-0.48160.8999-0.65330.8170.7169-0.64480.23890.9674-0.28580.11880.6388-0.0440.434234.765638.220228.3794
237.3936-0.9559-1.92652.5026-0.21728.09730.251-0.1934-0.05150.6639-0.37242.2547-0.0972-1.07960.04620.8234-0.33090.14990.7715-0.14690.598530.562339.253226.5202
247.3954-3.9474-0.36147.2231-4.28783.9248-0.0964-1.1719-1.12141.9804-0.2202-0.46581.86431.09050.43121.3377-0.1214-0.02370.88580.16150.537845.311635.159430.9876
253.78191.23961.13342.75540.57269.34780.0110.16150.0548-0.6725-0.18710.18760.6113-0.34960.18540.2915-0.0259-0.01740.2125-0.01570.39776.427674.22570.41
267.10660.1720.80022.2691-0.74423.157-0.18230.44251.1123-0.53310.39440.0475-0.07450.26370.3130.2953-0.03270.03750.22150.17010.570111.477680.4963-1.9989
275.22653.3066-3.90544.7945-0.56484.2519-0.32720.5109-0.3673-0.94660.388-0.04440.67070.0911-0.0260.3601-0.0180.04630.42640.0460.500417.981375.4048-2.6715
282.08560.5427-0.83573.1658-0.4754.18590.3566-0.5450.41991.1119-0.39950.2917-0.72090.0219-0.06330.6035-0.20280.02530.4759-0.06580.348210.552390.560820.9762
292.5394-1.4344-1.41646.83540.18345.44620.4316-0.52640.24421.681-0.3309-0.4369-1.51690.9017-0.11.2238-0.450.06880.9778-0.02470.47688.657889.554932.797
308.9558-0.75521.16716.8604-0.13487.70941.39920.14261.2781.6591-0.01551.6832-1.905-1.3593-0.33891.17310.02020.4410.80210.06860.7396-0.978894.187326.275
314.90662.77520.08821.77240.11086.4149-0.0208-0.1503-0.32760.7189-0.1813-2.00540.53981.20230.08530.3281-0.0029-0.16880.46770.15220.647627.011287.08629.1488
324.01950.9593-1.52184.86781.50299.14550.01770.092-0.0379-0.58650.0144-1.07080.01760.7079-0.09440.2452-0.06710.0450.28290.09190.504623.481688.37960.459
335.27250.6738-0.37556.5229-0.43293.4661-0.0384-0.5615-0.47780.430.07180.17090.29280.0824-0.06220.2223-0.06070.02020.3050.06580.289210.004576.795210.9231
342.4372-1.1602-3.24646.0546-0.69384.99540.2312-0.7989-0.49641.0085-0.41490.47820.31850.08650.21480.6515-0.1735-0.00840.66430.09530.4274.072170.694927.3942
351.9921-4.1779-0.72423.33082.63773.0893-0.1565-1.0323-2.3971.0746-0.5355-0.06290.82060.4891-0.11721.24430.1548-0.15141.16980.48560.581711.581864.906335.015
366.2938-0.96110.697.1541-1.06215.728-0.0236-0.1789-0.44130.10580.0488-0.2054-0.2812-0.26270.00550.17630.0056-0.00290.2038-0.06120.31923.550846.0928-1.9381
376.16681.9318-1.16137.78783.19768.29790.6286-0.14180.6077-0.6005-0.1709-0.0604-1.223-0.0867-0.36680.91490.090.22630.81520.08130.545633.141758.0107-27.8755
384.6251-2.9959-0.46428.18071.93284.8963-0.14940.3525-0.449-0.4491-0.07321.2365-0.2564-0.60360.2490.2847-0.0072-0.07530.3744-0.01750.414317.58350.5038-9.6115
398.50070.3957-5.45239.3947-0.76068.8829-0.696-0.1522-0.8939-0.50040.0797-0.55660.9671-0.3320.54740.88440.00970.1150.7989-0.04820.555232.128535.6447-31.4059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 30 )A-1 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 77 )A31 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 92 )A78 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 158 )A93 - 158
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 30 )B-1 - 30
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 55 )B31 - 55
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 77 )B56 - 77
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 103 )B78 - 103
9X-RAY DIFFRACTION9chain 'B' and (resid 104 through 159 )B104 - 159
10X-RAY DIFFRACTION10chain 'C' and (resid -1 through 30 )C-1 - 30
11X-RAY DIFFRACTION11chain 'C' and (resid 31 through 55 )C31 - 55
12X-RAY DIFFRACTION12chain 'C' and (resid 56 through 77 )C56 - 77
13X-RAY DIFFRACTION13chain 'C' and (resid 78 through 92 )C78 - 92
14X-RAY DIFFRACTION14chain 'C' and (resid 93 through 115 )C93 - 115
15X-RAY DIFFRACTION15chain 'C' and (resid 116 through 141 )C116 - 141
16X-RAY DIFFRACTION16chain 'C' and (resid 142 through 158 )C142 - 158
17X-RAY DIFFRACTION17chain 'D' and (resid 0 through 30 )D0 - 30
18X-RAY DIFFRACTION18chain 'D' and (resid 31 through 55 )D31 - 55
19X-RAY DIFFRACTION19chain 'D' and (resid 56 through 66 )D56 - 66
20X-RAY DIFFRACTION20chain 'D' and (resid 67 through 77 )D67 - 77
21X-RAY DIFFRACTION21chain 'D' and (resid 78 through 92 )D78 - 92
22X-RAY DIFFRACTION22chain 'D' and (resid 93 through 129 )D93 - 129
23X-RAY DIFFRACTION23chain 'D' and (resid 130 through 141 )D130 - 141
24X-RAY DIFFRACTION24chain 'D' and (resid 142 through 159 )D142 - 159
25X-RAY DIFFRACTION25chain 'E' and (resid -1 through 18 )E-1 - 18
26X-RAY DIFFRACTION26chain 'E' and (resid 19 through 30 )E19 - 30
27X-RAY DIFFRACTION27chain 'E' and (resid 31 through 55 )E31 - 55
28X-RAY DIFFRACTION28chain 'E' and (resid 56 through 103 )E56 - 103
29X-RAY DIFFRACTION29chain 'E' and (resid 104 through 141 )E104 - 141
30X-RAY DIFFRACTION30chain 'E' and (resid 142 through 159 )E142 - 159
31X-RAY DIFFRACTION31chain 'F' and (resid 0 through 30 )F0 - 30
32X-RAY DIFFRACTION32chain 'F' and (resid 31 through 55 )F31 - 55
33X-RAY DIFFRACTION33chain 'F' and (resid 56 through 77 )F56 - 77
34X-RAY DIFFRACTION34chain 'F' and (resid 78 through 148 )F78 - 148
35X-RAY DIFFRACTION35chain 'F' and (resid 149 through 162 )F149 - 162
36X-RAY DIFFRACTION36chain 'G' and (resid -1 through 77 )G-1 - 77
37X-RAY DIFFRACTION37chain 'G' and (resid 78 through 158 )G78 - 158
38X-RAY DIFFRACTION38chain 'H' and (resid 0 through 92 )H0 - 92
39X-RAY DIFFRACTION39chain 'H' and (resid 93 through 161 )H93 - 161

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