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- PDB-8vzf: Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase ApbHACS fro... -

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Basic information

Entry
Database: PDB / ID: 8vzf
TitleCrystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase ApbHACS from Alphaproteobacteria bacterium in the Complex with THDP, Coenzyme A, and ADP
Components2-Hydroxyacyl-CoA Lyase/Synthase
KeywordsLYASE / 2-Hydroxyacyl-CoA Lyase/Synthase / acyloin condensation / oxalyl-CoA decarboxylase / SBC / eBERlight
Function / homology
Function and homology information


oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / fatty acid alpha-oxidation / thiamine pyrophosphate binding / peroxisome / magnesium ion binding
Similarity search - Function
TPP-binding domain containing protein HACL1-like / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-FYN / THIAMINE DIPHOSPHATE / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesAlphaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsGade, P. / Kim, Y. / Endres, M. / Lee, S. / Yoshikuni, Y. / Gonzalez, R. / Michalska, K. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Commun Chem / Year: 2024
Title: Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family.
Authors: Kim, Y. / Lee, S.H. / Gade, P. / Nattermann, M. / Maltseva, N. / Endres, M. / Chen, J. / Wichmann, P. / Hu, Y. / Marchal, D.G. / Yoshikuni, Y. / Erb, T.J. / Gonzalez, R. / Michalska, K. / Joachimiak, A.
History
DepositionFeb 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-Hydroxyacyl-CoA Lyase/Synthase
B: 2-Hydroxyacyl-CoA Lyase/Synthase
C: 2-Hydroxyacyl-CoA Lyase/Synthase
D: 2-Hydroxyacyl-CoA Lyase/Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,56931
Polymers239,1524
Non-polymers7,41727
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33690 Å2
ΔGint-298 kcal/mol
Surface area67860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.800, 178.131, 196.482
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 , 1 types, 4 molecules ABCD

#1: Protein
2-Hydroxyacyl-CoA Lyase/Synthase


Mass: 59788.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alphaproteobacteria bacterium (bacteria)
Gene: DCO82_10540 / Plasmid: v53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A3C0TX30, oxalyl-CoA decarboxylase

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Non-polymers , 9 types, 363 molecules

#2: Chemical
ChemComp-FYN / S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE


Mass: 795.544 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H36N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 99068 / % possible obs: 97.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 32.67 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.111 / Rrim(I) all: 0.288 / Net I/σ(I): 6.21
Reflection shellResolution: 2.36→2.39 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.126 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 4335 / CC1/2: 0.548 / Rpim(I) all: 0.518 / Rrim(I) all: 1.25 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→47.35 Å / SU ML: 0.3345 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 4893 4.95 %
Rwork0.2073 93957 -
obs0.2093 98850 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.18 Å2
Refinement stepCycle: LAST / Resolution: 2.36→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16725 0 458 336 17519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003117598
X-RAY DIFFRACTIONf_angle_d0.671923949
X-RAY DIFFRACTIONf_chiral_restr0.04492547
X-RAY DIFFRACTIONf_plane_restr0.00463167
X-RAY DIFFRACTIONf_dihedral_angle_d13.85496507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.380.36921360.33222653X-RAY DIFFRACTION82.83
2.38-2.410.35121340.30732782X-RAY DIFFRACTION86.12
2.41-2.440.33091560.29392777X-RAY DIFFRACTION88.96
2.44-2.470.33741640.29072882X-RAY DIFFRACTION90.52
2.47-2.510.3311530.28852950X-RAY DIFFRACTION92.43
2.51-2.540.31651720.27123025X-RAY DIFFRACTION95.23
2.54-2.580.3261610.27873107X-RAY DIFFRACTION97.12
2.58-2.610.33551750.28713103X-RAY DIFFRACTION98.17
2.61-2.660.35351650.27153196X-RAY DIFFRACTION99.5
2.66-2.70.29581730.26863189X-RAY DIFFRACTION99.7
2.7-2.750.31721410.26563165X-RAY DIFFRACTION99.1
2.75-2.80.29391630.26493182X-RAY DIFFRACTION98.5
2.8-2.850.29511850.24723160X-RAY DIFFRACTION99.91
2.85-2.910.28191590.25443219X-RAY DIFFRACTION99.59
2.91-2.970.29111590.24053186X-RAY DIFFRACTION99.88
2.97-3.040.28061760.24543202X-RAY DIFFRACTION99.79
3.04-3.120.28331740.24443182X-RAY DIFFRACTION99.67
3.12-3.20.28071810.2443181X-RAY DIFFRACTION99.59
3.2-3.290.28891650.233211X-RAY DIFFRACTION99.53
3.29-3.40.26741590.21673163X-RAY DIFFRACTION98.72
3.4-3.520.23871660.20423223X-RAY DIFFRACTION99.09
3.52-3.660.25551710.19253228X-RAY DIFFRACTION99.47
3.66-3.830.24111470.18083221X-RAY DIFFRACTION99.47
3.83-4.030.22781670.16833201X-RAY DIFFRACTION99.2
4.03-4.280.20541940.15973217X-RAY DIFFRACTION99.16
4.28-4.610.17771570.14663195X-RAY DIFFRACTION97.9
4.61-5.080.18281660.14413251X-RAY DIFFRACTION99.1
5.08-5.810.18971440.16553293X-RAY DIFFRACTION98.54
5.81-7.320.19081520.1663256X-RAY DIFFRACTION97.62
7.32-47.350.15151780.14943357X-RAY DIFFRACTION95.98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6370369436660.05614504387040.3655556757590.426986229465-0.6089331359510.8863371247740.06053324441280.1692494686570.00537422455212-0.0470118936105-0.0447462856816-0.003991630695530.02637229319950.148942200764-0.01182699790730.2803527263810.02277456303430.006762620954770.438384928297-0.02893279516360.214783398129-11.497899154714.1886442094-20.1431735488
20.82099218068-0.3030801656680.5784536333010.514293272034-0.3173115920030.827904132714-0.09955218676650.2137993500140.08162243306740.03955998980080.0182696056865-0.0460758350579-0.003094618702060.2884820113510.07695744733450.408874080438-0.02187997673620.01370113694870.5135070663010.02081831298450.216935786895-25.163954291721.1675636983-41.3898270853
32.45438755849-0.5243399880670.9370951367562.647716416580.3622954551780.476785978893-0.131095623941-0.05323162955420.239985921737-0.1081813401570.152448958485-0.110071958836-0.01143462434350.239014244496-0.04649462938620.380221800881-0.00503447930744-0.002161112878470.3880408438470.02505534772460.247080850046-36.171452383634.283598183-39.8857136077
40.5313909587290.01819166576360.1115072173510.835317124979-0.2022792311591.417385540410.0817814890859-0.00326547605990.02494908847460.0229121262962-0.07206730743910.1599592333470.124079016202-0.2314218997780.02211358354470.287667096499-0.02367614163840.005877305975050.416963051397-0.007854270398580.195869774549-43.538908832121.41283731-37.8679770918
50.768229184502-0.011774844947-0.003494591720820.5793229729110.1833139170.103889331514-0.02093201658920.1170447608390.136761216341-0.061513983019-0.0720352162844-0.00457103654422-0.1816056094420.2045018599660.09998383595140.3201727507350.0176042763131-0.01169362508130.378515726265-0.004837771155550.212182228234-38.189006041435.2769265376-27.6087655947
61.727354640450.938065242673-0.2660440679863.32390678456-0.9219463329470.2320707013550.13116648463-0.09114256613940.2399849668270.314581040840.04984497451880.365775879538-0.241807439029-0.375553095269-0.1829757906480.382447361701-0.01495622229920.03674145483410.436721585071-0.03146487940580.211170335649-33.952890678129.2969344977-5.78158102061
70.396552396730.3236815603450.3188176892291.019014724680.8040823072360.604678197597-0.0736203100205-0.09280881457890.144618786829-0.144206927401-0.03350339922580.154083751361-0.0258992415057-0.2167336513980.06363907646530.329189127370.06023070083790.003584016543660.486100843223-0.00444912248030.238060350158-36.858288237836.9414620954-7.88741926695
80.542210344957-0.0533682407688-0.5537025008971.20444806561-0.1183534623491.488532906990.154499440198-0.01889970649640.02249554217740.0131273230749-0.1103063243110.21162822398-0.00180181962111-0.121460558322-0.02609358175510.2475569417470.01939714888950.01558562968840.486804135053-0.005819424701380.249120295979-48.78920189529.38275477281-1.51381265288
90.5166400452320.13131424757-0.3007047355950.5439611567680.007253407438860.2694271730490.112535626824-0.1097899115540.02027603127140.0561990035269-0.08353185269720.06840496432420.0456635771747-0.0605724107226-0.01029400725240.3048290556370.0390159397556-0.01268645142490.474444248517-0.007227973280730.22713132623-36.05470771082.9966252271-8.79484603606
100.561852595083-0.1743796215410.291577687020.392395443321-0.2795330157260.285818897611-0.01059985061810.07177233239940.01552527577280.0533818176227-0.0761235759867-0.03937304872870.05269977098930.06305867163120.07672008684410.317734531491-0.00428500258016-0.005414661679610.4670824650360.001389631321860.187899847216-16.2960669711-8.628417131219.84033999406
110.2736483352540.03926766801750.2960502461950.620787840899-0.1537125090060.439022152194-0.0267619900528-0.07257851250470.002198526235220.02138109766310.0135804609288-0.08444967977220.0003969928095320.01118577487440.007624001604960.3507482929420.00158595973429-0.01268456313420.553141074768-0.009985664361770.216814609416-13.68722450266.6284766397315.9511665007
122.573118814140.8302046543050.2051253745061.490353932130.2983570495721.65796492243-0.0189023282236-0.36331543915-0.109939881896-0.256448721238-0.182301853836-0.141915098586-0.2881940856350.2720512980180.1689471054380.329766940081-0.04099927682120.003873695475710.4107761533870.01794494244490.234209768049-21.702909424722.54253578624.65057783894
131.00352490675-0.910657849937-0.5174281250761.820514202220.7975426725631.759943088450.027130021878-0.1206475468480.1747384172930.1264944580860.0204659745134-0.230771027545-0.2050155008380.13823695531-0.03391874514360.309259776624-0.0788761979778-0.05237450757720.343141294597-0.01999043494140.22035375811-13.962403825325.77703978397.75555288387
140.7737080444660.2361028429820.9146303593891.71785161091-0.3595965830191.348904594570.0705637957677-0.1483133341510.0268200351209-0.152920769195-0.0810871518838-0.09212136818290.165636733320.125337345757-0.007502718360280.324617188430.115159910560.0382546499660.557974959687-0.01171756448520.210571160028-2.12171085636-24.1523614763-24.0224706045
150.51875377748-0.05118562866970.3788451656370.469036116096-0.3483296343730.4653370427760.03517407530430.02875833541970.08290258373070.01792381555280.0308358389356-0.0500842059070.0754314397260.0643207262873-0.06868553015910.3309447339890.0247252516285-0.01565336735120.489367863395-0.02381561377850.218764535294-15.6539421534-14.8485141258-20.5870841958
160.3391564049270.128756578828-0.01458346162890.4171279526510.07392262933610.9897330823220.0119450252163-0.0852906184614-0.05839029940380.037967072001-0.04535565499220.05854687753990.208947606412-0.175343769970.03161185374650.407945192623-0.03175384837860.004949301708660.4848758702070.02790838708550.257003783787-36.810118126-32.612487869-7.7553736078
170.934849166277-0.49537416094-0.6941406737661.76214056873-0.1057501841380.7496710947230.1164445470960.106821947867-0.0869839031368-0.556860754251-0.002474727860140.168690760275-0.05800141765230.0184077094679-0.1220834191060.460213998680.0132952884032-0.04964650189720.633463384155-0.06929153010050.238806301453-33.7527777129-32.8566502122-36.2062164075
181.11764785458-0.309900339274-0.8919757670341.017715489131.108589242451.45019151422-0.09474653808440.2645264174790.00362638248321-0.00515102457517-0.01119373694640.1076115725230.233526528954-0.2979513131260.0997642796740.488155530631-0.0219075339191-0.0164153730970.447045535588-0.03127487611830.240926195962-36.7195669615-40.5366452097-34.0726573412
191.075609296250.1639140461330.1844995886880.351995724746-0.07364261364720.1502866644720.00307847969264-0.130840721491-0.00372896335078-0.04211522742990.001364163414720.08388123557510.06595233874430.0272598775532-0.007240532207560.3303774153890.00552644216092-0.02744186693080.467802804784-0.04019045594270.226815771062-40.1024361786-8.72322161949-35.2648696956
200.652171186004-0.121715970155-0.03349567675630.481747231025-0.2166092241830.6518661798180.0133781312715-0.02762934661640.0108674996596-0.0969165231527-0.0768775886369-0.0284587859439-0.07188659585960.1041114853650.0765585748610.3937354173150.0186115882652-0.01266305275240.49065288911-0.01743179462570.232947135897-15.85050245445.18682350086-51.6648088348
210.5450121091380.0175591622427-0.514858388451.405249684590.5888022186631.83747549110.03747329326670.06690281068510.123452617322-0.2881980226330.0611188947793-0.248326602194-0.1105662962390.17422654479-0.09064892071790.338153378002-0.01243308108920.02215898735120.629217394459-0.01155471401680.155902267209-6.789166203062.88982483067-63.3092155287
220.142134056123-0.136041357621-0.265213503741.137658909030.3058287183980.5579843921930.02547981219460.0527426944837-0.0842222253239-0.280263556399-0.001826897664180.005759498845720.04297175842410.0762239493591-0.02349987317720.4037535344240.0213148086045-0.01862763632780.543938054824-0.02100684076530.208270640633-17.5908391365-18.6469952911-53.3036094837
231.587238815970.615412126495-0.2422133745731.483483590640.4283504987633.024479328220.1347830283590.171425985663-0.2479641035870.094959911874-0.196766104325-0.07655754654710.433877899340.1222111833970.02564895314770.5117232263720.0199221755381-0.00839806059480.338981171317-0.02210989989860.209908712469-18.0454218555-30.9241907429-43.6517508344
240.7570884439060.317124939234-0.3850299010350.971271538244-0.2851552200091.24896986862-0.1120261575580.00069432908218-0.161436533226-0.03715083407260.0335372345026-0.1567609202120.1466786754650.03005525263220.1113631420420.4274958955690.07087551661390.003270001516940.546192046082-0.05245830333630.244166407919-13.0459389547-26.7295922269-53.6236692003
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 170 )AA-2 - 1701 - 173
22chain 'A' and (resid 171 through 223 )AA171 - 223174 - 226
33chain 'A' and (resid 224 through 250 )AA224 - 250227 - 253
44chain 'A' and (resid 251 through 318 )AA251 - 318254 - 321
55chain 'A' and (resid 319 through 438 )AA319 - 438322 - 441
66chain 'A' and (resid 439 through 491 )AA439 - 491442 - 494
77chain 'A' and (resid 492 through 554 )AA492 - 554495 - 557
88chain 'B' and (resid -2 through 53 )BG-2 - 531 - 56
99chain 'B' and (resid 54 through 169 )BG54 - 16957 - 172
1010chain 'B' and (resid 170 through 318 )BG170 - 318173 - 321
1111chain 'B' and (resid 319 through 438 )BG319 - 438322 - 441
1212chain 'B' and (resid 439 through 481 )BG439 - 481442 - 484
1313chain 'B' and (resid 482 through 554 )BG482 - 554485 - 554
1414chain 'C' and (resid -4 through 53 )CN-4 - 531 - 58
1515chain 'C' and (resid 54 through 170 )CN54 - 17059 - 175
1616chain 'C' and (resid 171 through 438 )CN171 - 438176 - 443
1717chain 'C' and (resid 439 through 491 )CN439 - 491444 - 496
1818chain 'C' and (resid 492 through 554 )CN492 - 554497 - 559
1919chain 'D' and (resid -2 through 170 )DT-2 - 1701 - 173
2020chain 'D' and (resid 171 through 318 )DT171 - 318174 - 321
2121chain 'D' and (resid 319 through 363 )DT319 - 363322 - 366
2222chain 'D' and (resid 364 through 450 )DT364 - 450367 - 453
2323chain 'D' and (resid 451 through 506 )DT451 - 506454 - 509
2424chain 'D' and (resid 507 through 554 )DT507 - 554510 - 557

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