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- PDB-7mpp: Bartonella henselae NrnC cleaving pGG in the presence of Mg2+ -

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Basic information

Entry
Database: PDB / ID: 7mpp
TitleBartonella henselae NrnC cleaving pGG in the presence of Mg2+
ComponentsNanoRNase C
KeywordsRNA BINDING PROTEIN / RNase / bacteria / enzyme
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / 3'-5' exonuclease
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI142400 United States
CitationJournal: Elife / Year: 2021
Title: Structural characterization of NrnC identifies unifying features of dinucleotidases.
Authors: Justin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann /
Abstract: RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NanoRNase C
C: NanoRNase C
E: NanoRNase C
G: NanoRNase C
I: NanoRNase C
K: NanoRNase C
M: NanoRNase C
O: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,77440
Polymers187,5748
Non-polymers6,20032
Water20,6091144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32210 Å2
ΔGint-324 kcal/mol
Surface area62980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.929, 126.734, 127.145
Angle α, β, γ (deg.)90.000, 94.278, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
NanoRNase C


Mass: 23446.725 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BM1374165_00260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5MEI1
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Succinic acid; 10% PEG 3,350; 20% xylitol, 5 mM MgCl2 (soak)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→126.8 Å / Num. obs: 148330 / % possible obs: 98.14 % / Redundancy: 4.2 % / Biso Wilson estimate: 33.48 Å2 / CC1/2: 0.992 / Net I/σ(I): 18.57
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 14541 / CC1/2: 0.444

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.15.2_3472refinement
pointlessdata scaling
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yt3
Resolution: 2→126.79 Å / SU ML: 0.1962 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2459
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1872 2004 1.35 %
Rwork0.158 146209 -
obs0.1584 148213 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.77 Å2
Refinement stepCycle: LAST / Resolution: 2→126.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13069 0 400 1144 14613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005913918
X-RAY DIFFRACTIONf_angle_d0.827918946
X-RAY DIFFRACTIONf_chiral_restr0.05312153
X-RAY DIFFRACTIONf_plane_restr0.00442406
X-RAY DIFFRACTIONf_dihedral_angle_d15.77678407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31671380.262410285X-RAY DIFFRACTION96.9
2.05-2.10.27951420.25210158X-RAY DIFFRACTION95.49
2.1-2.170.24921550.192710497X-RAY DIFFRACTION99.02
2.17-2.240.23331290.187410516X-RAY DIFFRACTION98.86
2.24-2.320.26551400.196110286X-RAY DIFFRACTION97.06
2.32-2.410.21441560.170310441X-RAY DIFFRACTION98.9
2.41-2.520.22091330.172810408X-RAY DIFFRACTION97.55
2.52-2.650.19641330.163210547X-RAY DIFFRACTION99.29
2.65-2.820.19431560.16610525X-RAY DIFFRACTION98.67
2.82-3.040.20141390.173710535X-RAY DIFFRACTION99.45
3.04-3.340.22671470.164510437X-RAY DIFFRACTION97.65
3.34-3.830.15941460.141810482X-RAY DIFFRACTION98.41
3.83-4.820.14251470.117210419X-RAY DIFFRACTION97.54
4.82-126.790.14771430.147310673X-RAY DIFFRACTION98.55
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)
13.394545221760.19243845105-1.623079705192.99354902654-1.101243692274.01319467235-0.0338378294754-0.07077982880550.05243055178360.3716116928750.02643379194260.351313484703-0.32595698176-0.2433371884290.004711765107820.2697072098090.07791243966920.01951203343110.235380772635-0.01204066686610.217808408889-14.3918002335-7.7777250041657.332085897
20.875577032106-0.1566595043030.08584012441063.20869751914-0.0883195649210.4695842480960.030764072658-0.0861183758226-0.0522819337620.228580503789-0.04107793144350.183381398574-0.0909331648587-0.09956484036150.02104345000560.2546766618010.03640802444080.04023201671470.2414199269110.005067910745890.226282163383-8.64087100689-19.889085693957.5234546053
32.442888890231.85313641116-1.569149091729.28513166953-1.880313037687.46481970298-0.4196049981410.612965253758-0.12428111996-0.266515952880.232233670418-0.0248507360819-0.346766396613-0.3398535608840.2139446060860.2859616572720.0487601403368-0.018396907510.391322213558-0.02274070104620.279397865638-18.3260153778-9.1607697056444.5536565897
41.24236435564-0.0361301966613-0.1711655638441.80264050064-0.006828473806540.551496739162-0.0670982438553-0.0338029903085-0.09349541489340.296103899509-0.01619026640990.069196393051-0.010052996789-0.05228260535760.08295106170940.2899640932080.0289904686950.01114412130350.2282077875870.002596741764930.209553536353-2.83321380907-24.131780913659.0995872658
51.802158319880.821346672385-0.1284902352733.496425663020.8947571214732.5760844948-0.01283949624040.0688866329683-0.1072446050.1772594618690.02756262081690.146838355960.250763069435-0.3174477823220.01076651353590.244793747097-0.02871165219970.03622836548170.282983153840.04524424774230.333371125664-13.3362503187-56.459439060152.9125451267
60.5852586740340.04031920749710.05889699255271.078972533410.0239253640853.95022708585-0.02852398714990.09037111467060.03598490450290.004842917869290.0259771416230.132883296260.0636729794828-0.258643300446-0.01288721001770.195076296226-0.03466137102910.006112540810630.2622711252730.02858955858790.295291998874-6.89776075831-56.132216444541.5363179106
72.369312013350.6627929056250.6195252668266.652766721425.130247082365.70777434278-0.2124792870920.208370981580.519633920274-0.3726251535070.04185353426550.503197754644-0.379930190352-0.3643173065320.1379197551330.2293078159890.000829226621586-0.01087594536980.3399511124760.0860928852590.475365842848-17.9632950372-47.462987665748.4105648564
81.566824000710.2433071217941.137231047851.503228781710.4205157922963.378287109860.0456426263826-0.0309844723813-0.04082657214390.0170778287566-0.00675718800484-0.05384487118250.256489029229-0.146871869425-0.04661185428970.1749997457740.004598760031460.02259209003980.2058780248750.03733522098780.2582657355072.09354817375-57.672132053536.5462906654
92.55877716684-0.863820264872-0.4654666124912.067930098160.7543828024212.664988927920.03992146266640.2423995503490.0806133600703-0.437383781914-0.06559433637780.147579623361-0.522456428463-0.2860383288470.03212318807680.4638870141520.0196369943539-0.1035892578240.283744537514-3.23567910878E-50.237705822672-10.8419738904-3.650385997388.73040510099
101.08090537894-0.271935219991-0.1824629837660.6425219802720.434824967763.196755509160.02312411953410.146142339211-0.010954182568-0.229222411962-0.00826382699980.121115262355-0.375438984287-0.0986289245124-0.01933221871140.3142355065990.000409646399672-0.05686209929860.210242904926-0.01843496834620.198366548787-5.89008812543-3.5750687916721.2583479062
116.82989660342-0.935889280147-3.567564628295.284854778252.557655346822.69455563071-0.2388971413870.212025976909-0.625980034676-0.109523424056-0.07243896859640.4820073082160.0815381301971-0.2457289519240.2684959980380.384888818767-0.0445450784154-0.0701861357660.317303489112-0.03263464369610.401285681749-15.8684153771-15.697882343310.7646293729
121.487865371690.04832242796620.07447278203930.178506504578-0.1055997082271.22376195937-0.0825271006128-0.0254505995336-0.03302145037280.02254020058220.04579919718020.0756287759355-0.3039606562170.02552603548870.02234937879310.413737796045-0.0158885848728-0.03647286173680.2505078436230.002371869406120.225860727505-0.746089003101-2.2562380293626.2579247648
132.09830797842-1.26004307950.7652100695992.75653733858-0.1355793064882.25061345159-0.180904944729-0.1050144635020.01474367721390.5252593454230.08829146958-0.24139327382-0.09900044173320.2049580852610.0824805854130.2979671267440.00120567621725-0.1132132464850.2957235298530.08372358355010.38071383477225.9187367232-37.382000521268.0463020769
141.524603750010.5671846569610.3757567845594.73539640642-1.201613729751.57777246157-0.01285433255120.108279194447-0.2020456711230.059609939046-0.0852367921371-0.417050167371-0.1088800078150.1573048221420.1181391953230.2203734179760.0144458459214-0.06096321557160.268826689790.03466763511410.31155827414322.4248608091-26.365456658657.4883269958
156.586919892182.74007455702-1.000279512582.14071038044-0.8624194014056.27370337618-0.2506442768530.648946521833-0.0264669581433-0.4722491766560.186841531292-0.357335868924-0.1500591339680.5083107678820.02490858759570.2488078913730.0187450506307-0.06837604889640.511982159895-0.01431293457170.51719983650833.2610841525-42.17973638555.1883423911
162.167620236510.153728869760.1895954189161.93325713741-0.2431049910281.06121661087-0.00984525871364-0.108731189824-0.1272190717980.234310813588-0.0413762953905-0.236733972583-0.1984714601340.0965129952020.05132646323830.293439330964-0.00377392714665-0.05951901436810.2515575348450.04020770326360.22098803916516.168814591-23.576190920260.3652570228
172.004027043730.386832580044-0.3255962723943.15018435577-0.726514765782.3492767038-0.0474088099790.0950081694435-0.00624654867863-0.6172726362570.02166140727850.2670720402880.168904458329-0.1278753889190.0226025969120.370436435742-0.0417835890686-0.04461977622350.254688491328-0.03877849100590.245717759675-8.18827673412-51.16287804422.77930049681
181.45476774895-0.5158585314860.9104624873713.94434361027-0.8972657828560.727035688412-0.0583320466411-0.1990983136650.0248103976484-0.03770965991280.08569830114630.149822178436-0.110029313323-0.0571621850611-0.03176057604820.324038773851-0.02278015624880.01951609582110.279501087776-0.03831469145920.23213474828-5.2028048825-36.72318535748.23490898024
195.30990494508-2.766442189690.06922984080456.69790640895-1.031213973146.17880224117-0.204353733283-0.297959130091-0.07022950942580.4030158260870.1409667602620.637081027213-0.170442582913-0.294180279480.08969704921510.223549359212-0.05244473189770.01466961674750.490455903393-0.02271843967950.323366099665-15.6717772012-50.523625818816.4029330377
201.287615593030.2552383784240.05145730805352.246478982560.2530510165380.0917912294622-0.0811268935829-0.0204627899134-0.0240631212173-0.5034720362150.0665013711914-0.0046449306109-0.106268544099-0.02437663373240.02138787674870.379897914877-0.02655255913870.0154842774570.315340879717-0.05434215766210.2428641791381.25618296251-35.33573998084.23664077802
212.159432141330.0891959031978-0.4621761756381.16574409652-0.1555711784913.4470855869-0.0926668344610.0963001707943-0.148001740806-0.1630594265130.0340407765087-0.6546328799330.6883839458960.4073546393730.06956397366060.3485110145090.1011357633510.1286737285180.410406252806-0.01957566879650.67533114414130.75939466-62.724920068723.8462326123
221.52989998496-0.0938611799924-0.1222473586870.8515221979340.4282441898294.10996476051-0.06042583254270.0746789636669-0.225938445604-0.103059969336-0.0228091329813-0.3662977360650.5271794330040.0555959894490.06398191133860.2842916271890.04063026435210.0628553374490.337508093267-0.006543043713250.53098699597321.8087846886-63.715844645130.3698288531
230.733674448274-0.18000882149-1.368224475840.5817661466650.2942435845764.45183711590.1055270839510.006432394961820.267370901192-0.110477287780.0727631935292-0.579649840114-0.328223739290.590273338634-0.184596454020.257505850263-0.01344331365280.02916621831910.4870886997020.04320383983230.75655524136631.4495691454-48.588134179533.1031857958
241.41632046363-0.264579372542-0.5176141486691.640368947810.4476008349521.90478156396-0.1149490310.0121427502386-0.02119640818220.1595239587790.044223038327-0.5048477691330.2311671096610.3413091482150.08230727857260.1995666317570.025581865952-0.01303396891280.2423143798220.02506706213790.42948533770919.3705620337-56.855795416838.0639381072
252.273125769380.3939587837640.2108769502621.59012253242-0.1927582066362.59494893201-0.151743149718-0.02391157250420.1530461569860.04455492130010.104996366557-0.155063076357-0.5004497902380.23465943720.03408055270550.374229793107-0.0894535068261-0.06956932570970.260744060144-0.002939998983090.2291006222626.75493844785.3775731940441.4523722266
261.7147593909-0.107613785424-0.4918972557171.27894895440.8406737472333.45364367622-0.0618005174571-0.0685652657355-0.1218895775120.07912671472390.0437736609383-0.1921816133250.02381146703440.2619158195710.01276514283640.267405310308-0.0735974166006-0.02892709027780.268724638675-0.002829408362740.25344459057424.2218557596-5.3998244912830.4956518051
272.27073711999-1.42151704553-2.060819385643.157447036013.235957231213.53268367697-0.316768893349-0.274097824564-0.812495877334-0.0275503994730.259181299644-0.09818762313890.06569903393690.6204473675210.1206605082070.36077038908-0.0279752888836-0.07710218233590.3890386653590.08460071316040.4639025785632.5872092285-8.4324752069448.0087314231
281.197954888010.007907795939550.1817785706650.5311359331050.05028694408091.02748323909-0.09509338009890.0370833550498-0.0687805396679-0.1402610325680.0192063640368-0.0851847777637-0.2255257231250.1298886589820.06753480131660.362883565362-0.0713579759919-0.01630360819220.278903320276-0.02072246607530.25358490560319.4426423833-2.2941881979127.9901078884
291.70915394626-0.226309046561-0.1929762543251.396588860261.129010347772.24763146672-0.3815891850010.411948603744-0.255654458498-0.8696362540.159281062899-0.477847663051-0.1911729777640.1894097490010.1243395065720.594879521692-0.2048378299470.304651348530.482384643639-0.09666777269380.44502808270231.4119064832-19.24038544330.101911227034
301.99670421408-0.706880234582-0.2875761860563.03501236557-0.2941651978080.708032254705-0.186741855270.297114960703-0.170634915213-0.7256182491880.190131286635-0.373146524627-0.02690471236220.03223065715010.02668331366570.478878280075-0.1446847211550.1693157587690.401615416933-0.08962830301560.368543305323.0258960203-27.74413960880.112589024496
310.9488161234021.928172803720.2526204835883.854456518950.3389778466581.036289194790.0487870845017-0.240649588289-0.4890569462480.0384864747586-0.140880053228-0.782509935164-0.08147444058920.2699080944520.0748193400520.251574035915-0.02751884319850.1255679131040.5592520076-0.02179097865240.53548757296633.3181771842-27.612684669714.5347096305
321.963214803820.1604272260660.247419288771.81903961648-0.1228759893621.03632418612-0.275815640232-0.00941154068057-0.289695476629-0.4882832501630.182680052452-0.4122007140790.1319273225830.2021028952860.09093330653950.370285036687-0.04070525634560.1747666329060.324297878925-0.04831425658680.33818486989120.4596403311-35.7651028485.66368743836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:61)
2X-RAY DIFFRACTION2(chain A and resid 62:131)
3X-RAY DIFFRACTION3(chain A and resid 132:151)
4X-RAY DIFFRACTION4(chain A and resid 152:206)
5X-RAY DIFFRACTION5(chain C and resid 2:60)
6X-RAY DIFFRACTION6(chain C and resid 61:131)
7X-RAY DIFFRACTION7(chain C and resid 132:160)
8X-RAY DIFFRACTION8(chain C and resid 161:206)
9X-RAY DIFFRACTION9(chain E and resid 2:60)
10X-RAY DIFFRACTION10(chain E and resid 61:129)
11X-RAY DIFFRACTION11(chain E and resid 130:151)
12X-RAY DIFFRACTION12(chain E and resid 152:206)
13X-RAY DIFFRACTION13(chain G and resid 2:81)
14X-RAY DIFFRACTION14(chain G and resid 82:130)
15X-RAY DIFFRACTION15(chain G and resid 131:152)
16X-RAY DIFFRACTION16(chain G and resid 153:206)
17X-RAY DIFFRACTION17(chain I and resid 2:81)
18X-RAY DIFFRACTION18(chain I and resid 82:131)
19X-RAY DIFFRACTION19(chain I and resid 132:151)
20X-RAY DIFFRACTION20(chain I and resid 152:206)
21X-RAY DIFFRACTION21(chain K and resid 2:61)
22X-RAY DIFFRACTION22(chain K and resid 62:106)
23X-RAY DIFFRACTION23(chain K and resid 107:148)
24X-RAY DIFFRACTION24(chain K and resid 149:206)
25X-RAY DIFFRACTION25(chain M and resid 3:81)
26X-RAY DIFFRACTION26(chain M and resid 82:131)
27X-RAY DIFFRACTION27(chain M and resid 132:148)
28X-RAY DIFFRACTION28(chain M and resid 149:206)
29X-RAY DIFFRACTION29(chain O and resid 3:65)
30X-RAY DIFFRACTION30(chain O and resid 66:107)
31X-RAY DIFFRACTION31(chain O and resid 108:152)
32X-RAY DIFFRACTION32(chain O and resid 153:206)

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