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- PDB-8ay7: X-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, ... -

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Basic information

Entry
Database: PDB / ID: 8ay7
TitleX-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, V168A)-iSB7-HAB1 TERNARY COMPLEX
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 16
KeywordsPLANT PROTEIN / CsPYL1_5M / HAB1 / Phosphatase ABA receptor inhibitor complex
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / START-like domain superfamily
Similarity search - Domain/homology
: / Chem-S5N / Abscisic acid receptor PYL1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.131 Å
AuthorsInfantes, L. / Albert, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Sci Adv / Year: 2023
Title: Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought.
Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. ...Authors: Lozano-Juste, J. / Infantes, L. / Garcia-Maquilon, I. / Ruiz-Partida, R. / Merilo, E. / Benavente, J.L. / Velazquez-Campoy, A. / Coego, A. / Bono, M. / Forment, J. / Pampin, B. / Destito, P. / Monteiro, A. / Rodriguez, R. / Cruces, J. / Rodriguez, P.L. / Albert, A.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 28, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40716
Polymers60,2992
Non-polymers1,10814
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.821, 62.724, 186.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Abscisic acid receptor PYL1


Mass: 23269.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g046151mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A067E666
#2: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37029.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 92 molecules

#3: Chemical ChemComp-S5N / N-((1,4-dimethyl-2-oxo-1,2-dihydroquinolin-6-yl)methyl)benzenesulfonamide / ~{N}-[(1,4-dimethyl-2-oxidanylidene-quinolin-6-yl)methyl]benzenesulfonamide;


Mass: 342.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 291 K / Method: microbatch / Details: 30% PEG3350 0.5M CaCl2 Drop 1:1 / PH range: 6

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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: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.131→44.21 Å / Num. obs: 28817 / % possible obs: 98.91 % / Redundancy: 5.9 % / Biso Wilson estimate: 46.85 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1141 / Rrim(I) all: 0.1255 / Net I/σ(I): 7.37
Reflection shellResolution: 2.131→2.207 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.306 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 2638 / CC1/2: 0.695 / CC star: 0.906 / Rrim(I) all: 1.443 / % possible all: 92.98

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Processing

Software
NameVersionClassification
XDS2019data reduction
XDS2019data scaling
PHENIX1.19.2-4158phasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5mn0

5mn0


Resolution: 2.131→44.21 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 0.63 / Phase error: 29.0721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2473 2649 4.96 %
Rwork0.1909 50759 -
obs0.1938 28817 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.68 Å2
Refinement stepCycle: LAST / Resolution: 2.131→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 57 78 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823917
X-RAY DIFFRACTIONf_angle_d0.94445293
X-RAY DIFFRACTIONf_chiral_restr0.0561591
X-RAY DIFFRACTIONf_plane_restr0.0055706
X-RAY DIFFRACTIONf_dihedral_angle_d24.17321456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.131-2.170.34061440.31162323X-RAY DIFFRACTION84.86
2.17-2.210.35421200.29152656X-RAY DIFFRACTION99.07
2.21-2.260.37841490.28772744X-RAY DIFFRACTION99.18
2.26-2.30.30061380.27162672X-RAY DIFFRACTION99.12
2.3-2.360.33181850.25992651X-RAY DIFFRACTION98.85
2.36-2.420.3731510.26022669X-RAY DIFFRACTION98.26
2.42-2.480.30681280.25472668X-RAY DIFFRACTION99.29
2.48-2.560.25411080.23782745X-RAY DIFFRACTION99.51
2.56-2.640.2965920.2362784X-RAY DIFFRACTION99.62
2.64-2.730.32281590.22462688X-RAY DIFFRACTION99.44
2.73-2.840.3411240.22332743X-RAY DIFFRACTION99.51
2.84-2.970.27751330.22082683X-RAY DIFFRACTION99.33
2.97-3.130.29691650.1932683X-RAY DIFFRACTION98.38
3.13-3.320.28731480.19212688X-RAY DIFFRACTION98.64
3.32-3.580.21911530.1712667X-RAY DIFFRACTION98.74
3.58-3.940.20661440.162675X-RAY DIFFRACTION98.88
3.94-4.510.19861300.15832657X-RAY DIFFRACTION97.35
4.51-5.680.20661350.16252662X-RAY DIFFRACTION97.69
5.68-44.210.2221430.17532701X-RAY DIFFRACTION99.16
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)
13.24899949545-2.378405586370.7304696489177.07610153496-1.285717445042.034037718730.15454768551-0.809437611727-0.1055500695920.7697351706590.0726259115175-0.3407459646470.495347398777-0.0938516847692-0.1636150211880.7937404562090.0721770701385-0.1457628726460.7243149687610.03469982986080.5013761590868.675729871637.448982976255.1851565943
22.72781569569-0.163671279575-0.2930387586532.28690691707-0.4526988689052.22783372098-0.00948338755305-0.126168767952-0.2534269156370.1188281981-0.0761592561984-0.2969023598740.3639233196910.520325821580.07382136385990.7148518940930.0856091570799-0.06275603082030.6194351510670.06759605378660.4683690162239.335253710724.5209917277544.8743765259
33.59850107479-0.954300489004-2.497605412281.653551158941.20445049137.49071584405-0.0689110939203-0.0306185723046-0.3440005743120.3320437383430.0425051025470.3609128517161.03792170096-0.6073583766760.03794657905220.519933885738-0.0858380677662-0.01582288487580.4342600642090.03764913070550.402337424532-7.094230824981.9332398342138.2838347527
42.162914415232.91243906471-1.070713983499.255895561620.7694413550776.79353323035-0.1320200576380.493277768037-0.5889553863650.2209263624180.278286674323-0.436391539108-0.0139633706713-0.197118659229-0.1510790354430.4664760140990.0012993853009-0.06210521967160.475499220365-0.02774539279340.4545155674846.905475016670.9050808674529.8439278928
55.820525297460.878340025453-0.4536361754192.758186434470.196543744095.914177020710.211771067477-0.2286410277790.2557056093680.591758063385-0.2696043369790.060872601320.172639413312-0.5097099092690.1695966271710.600494971413-0.0383974986194-0.01527152885920.3776753482360.07726781038720.3760473786892.729602367948.2424901300547.0234904752
62.65648440803-2.82518977205-7.22181633184.266555691852.30634221077.300774217520.738528545504-0.6043426538220.714228381225-0.253694173189-0.0478919556244-0.216821076198-0.08313981670040.525937138758-0.731586293480.582019911328-0.0090452904828-0.03432506872960.43108185876-0.0134105220080.330113224082.219964994213.64961791239.4235752722
72.074746990691.6173243418-3.6489104952.00949806732-3.033273303892.070077768230.162935665647-0.209098488791.097741815320.22141170054-0.1873459037490.641719433326-0.4400977816730.6183651178940.1058422828980.6038451021520.0442384028801-0.138628683730.443596539234-0.05042980802350.501574489549-7.3531714401132.9861886025-4.66244250337
81.277658471451.45171662-1.421156355032.080388584021.982135921562.06545480070.292372462518-0.332214657741-0.27169195748-0.430469248652-0.509262826652-0.3493545370880.9809701340570.9058286301620.3463076817590.3148084157150.0389741494411-0.06323303082480.4280141538960.05975970851990.354809355155-5.6125982961112.60545977247.8487675733
94.07479393345-3.84799300441.219566653032.20755311725-4.691318821017.01327704577-0.2588983475840.07919555157960.1199015810980.107923454604-0.242548421572-0.1426462995090.2681372792280.03455201432230.3237512690820.3228618995610.01209913804450.03314425789130.466561035552-0.0532112789960.399701207102-8.5329311907321.511242006910.0746866484
109.906065714568.677854268631.59250881122.067488059762.148997370248.41051284847-0.108332714157-0.1271826038511.839095723631.229433470931.033756637650.363127331151-1.125381522230.449538698025-1.094229501610.7873043670030.1857408931970.02964069855380.491364417603-0.1228258677770.756417670372-10.356107076741.05106860724.51159513351
112.04384026658-8.65693819698-6.145233713632.023179137272.02804756081.99780179035-0.7558543902180.666600136966-0.7230691054212.04895282656-0.4088407645551.145047200241.37633661349-1.533829624291.36526692540.876010410052-0.03430553991730.2321031385460.603978868785-0.1211725639390.756378430711-1.2544236417349.91797911835.0567547308
123.847505623451.95508928594-3.237977800890.948825588331-1.611346724322.596189494481.31501885815-0.2774627453580.09100369763162.1192045291-1.090215462591.36633307587-0.2441779015060.983505481499-0.2442937677671.10985607547-0.1378242806390.2219113170250.921638315265-0.2873304121611.267563665921.7422653061256.3678484362-2.28123861255
136.13851424546-0.2580426491751.675026023022.85401190688-2.293402420474.97796749880.2377563667460.4100482214691.448597725590.3271024591110.3690566438081.58239945134-1.31146522867-0.813296753606-0.5427076773220.5022138489370.1635832661290.0305769575520.7326488076350.2212557523820.690053301466-7.4399544679343.26983563421.34061974357
143.909744895430.83392274191-0.5616997006197.21943233329-6.695138056532.39009958738-0.182617215922-0.415279429116-0.1884540171-0.4115291907780.3503470222940.2025605086570.564153764829-0.826359082521-0.2070052011450.435445161866-3.43572341538E-50.005752848554180.323310568220.006649158859180.25268652104-5.1047899422423.550440271313.7042399984
153.719406675262.51044618374-1.11978019812.11793518244-3.703209333737.645099489460.425415310949-0.4684053073430.6819144744640.249979545544-0.4091033181470.639436624481-0.9618194547920.0385211995441-0.03308032288060.4466267695230.001490540478220.04441896784750.50107008511-0.07105191544070.455094093022-9.9767420929636.723880527715.8902832258
1610.23155990826.11529562294-6.011375176793.51600074733-6.211147789083.242386146280.2977820968460.234926294956-0.1516831530650.9654129111260.0907949723994-0.66181714897-0.8686353673040.0337778288872-0.3834340577910.7078268791790.01466093456580.009888287039280.563080097973-0.180029530280.566047531547-1.0253147762738.637292588618.4152878904
172.25872482314-2.25405588922-4.245973441212.05150419987-0.3681275603352.0203827444.05816895809E-5-0.94507333164-0.3509676373160.502721751002-0.0374771959824-0.1265094087490.58536367134-2.23089510635-0.04200010332810.9299648679170.0505185800328-0.05700975393130.9977707885930.144223337170.655636086641-12.721479086332.714506375628.0985129032
182.06886210183-2.545766162931.699537174456.33032537677-2.808762537072.69486498898-0.0452561706297-0.6146784290790.04124531645320.6127259433720.5937257735761.42541936165-0.43690892973-0.402961017395-0.4646124739680.602818004456-0.0284513048350.06258691417160.4559954094990.03135157593640.612472001844-6.6293860666829.287119428318.7744132376
192.10211219476-1.152125326130.049780550421.76620013513-0.4558914659523.49018480461-0.0152114532556-0.4145766503660.1566987219720.1746177283410.0363097557658-0.1692071381690.2580219762440.246489306026-0.000200154340190.424921013242-0.08997761773320.005006820426410.456390406168-0.03675532396170.3769971871198.4928164428928.81105580567.8096987657
208.79544342666-5.80956679472-2.223154583182.24507414099-0.5869696984582.10709566982-0.23482937092-0.2246638684070.6347391656150.103200089158-0.229380893682-1.16804635285-0.8410387293711.933563311760.4972849111830.587053327999-0.128196501196-0.03810955408150.601399964620.08489257756250.58357985310815.358286460527.516607567126.5905368475
219.31987512107-0.686123461444-0.03757065104552.262540033812.924941577433.586492017360.161388766563-0.141213637821-0.3038490506150.6172838424750.00497918828691-0.7425281927580.580588139090.835538678199-0.1669124477930.477950818970.0909327371673-0.02289058258310.6111046925130.08000168816240.37214829805211.78652819915.668699135327.7053184083
221.07063134106-1.233531429340.3206843060091.41174830126-0.3497792102190.0987637419330.0667848076935-0.0981696441549-0.1265193090360.212289154241-0.0943784144380.0825695680301-0.611385827274-0.1796598151040.0561688732570.549504317423-0.007298438651450.0005252615583880.5266185418940.05306421175710.3525406746233.6000010747322.987680323123.2138519635
235.57663651784-2.168010224631.919708932845.47658498813-3.770945480862.18068363688-0.50715424996-1.022232970150.4342552180350.3590893612560.473042335160.1705830569630.674577279845-0.797980822427-0.0311246503490.65262265404-0.0111206013342-0.03309576554560.559945002863-0.08898185578430.3585087549042.746589817227.296707438528.2379000413
245.983520116311.5592478336-3.381746222225.593355736581.207640822.09202082680.315022666689-0.08254052330740.68425425972-0.334657159246-0.0477385486289-0.335042431319-1.115948051861.31633692036-0.16780067560.400564821427-0.03851155047920.02585398523060.4239346502790.01369163193650.5329029510337.1267683837538.35084534871.73282591761
250.932662969888-1.475523410910.3677103579857.83687940135-5.685947703596.309769145450.149298611883-0.009430002794070.0482843522228-0.168984835076-0.387531651979-0.1556656688740.02320388615410.7077068888920.2289305935030.245416230721-0.0457481362317-0.02434604856850.457885002384-0.02253185937580.3728966926665.2183395541121.80916514542.96798538561
263.49278168835-0.003840772573964.796635216922.291690455350.4374321138773.063962373390.1697545054610.402891815991-0.71089720388-0.28478587180.112849018379-0.09348080449910.4160707704480.211100992002-0.2024977572880.39684996905-0.001859883829930.02659592745090.427627199789-0.01997383769660.3209298925223.2998435062721.3504154432-10.2003137371
271.10930629859-0.181670931744-0.9414802155812.38560230743-1.060511224088.133660997840.2702914657040.5543101961460.1516247753-0.84631013175-0.348897296731.04105931335-1.43572364167-0.106648788449-0.04185720052160.686016196897-0.0163861273274-0.09863374462970.571058503844-0.01371829209420.578026153795-11.752463100929.911367824-11.267737561
285.85364266753-6.63714680045.901710472282.48930608392-9.3158247304110.15814156570.5872823734970.0399501114483-0.824922029221-1.16826574892-0.04925297246510.8826301860591.09146826552-0.522272731605-0.5077734188840.393755543151-0.0800644513524-0.03019661359190.357285125449-0.03360000864450.408902917678-1.5809489159115.3975940427-3.61743493391
294.265056889850.351507549609-3.17077449675.453960182420.614514542632.80489550517-0.04181086942480.2518736140790.216048393385-0.2690090508470.4368868921680.253564532654-0.121917748795-0.511826391044-0.3856015528210.235622181573-0.0519867629421-0.0890920153430.3972668862040.001173087398970.327529967150.22734873572621.9290333445-0.585943802664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 181 )
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 207 )
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 190 )
8X-RAY DIFFRACTION8chain 'B' and (resid 191 through 200 )
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 210 )
10X-RAY DIFFRACTION10chain 'B' and (resid 211 through 215 )
11X-RAY DIFFRACTION11chain 'B' and (resid 216 through 221 )
12X-RAY DIFFRACTION12chain 'B' and (resid 222 through 232 )
13X-RAY DIFFRACTION13chain 'B' and (resid 233 through 237 )
14X-RAY DIFFRACTION14chain 'B' and (resid 238 through 248 )
15X-RAY DIFFRACTION15chain 'B' and (resid 249 through 273 )
16X-RAY DIFFRACTION16chain 'B' and (resid 281 through 302 )
17X-RAY DIFFRACTION17chain 'B' and (resid 303 through 308 )
18X-RAY DIFFRACTION18chain 'B' and (resid 315 through 337 )
19X-RAY DIFFRACTION19chain 'B' and (resid 338 through 368 )
20X-RAY DIFFRACTION20chain 'B' and (resid 369 through 378 )
21X-RAY DIFFRACTION21chain 'B' and (resid 379 through 392 )
22X-RAY DIFFRACTION22chain 'B' and (resid 393 through 402 )
23X-RAY DIFFRACTION23chain 'B' and (resid 403 through 413 )
24X-RAY DIFFRACTION24chain 'B' and (resid 414 through 423 )
25X-RAY DIFFRACTION25chain 'B' and (resid 424 through 439 )
26X-RAY DIFFRACTION26chain 'B' and (resid 440 through 458 )
27X-RAY DIFFRACTION27chain 'B' and (resid 459 through 471 )
28X-RAY DIFFRACTION28chain 'B' and (resid 472 through 487 )
29X-RAY DIFFRACTION29chain 'B' and (resid 488 through 505 )

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