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- PDB-9mno: Structure of the TelA-associated type VII secretion system chaper... -

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Basic information

Entry
Database: PDB / ID: 9mno
TitleStructure of the TelA-associated type VII secretion system chaperone LcpA in complex with the chaperone binding site of TelA
Components
  • DUF4176 domain-containing protein
  • LXG domain-containing protein
KeywordsCHAPERONE / Molecular chaperone / type vii secretion system / antibacterial toxins
Function / homologyLXG domain of WXG superfamily / LXG domain / LXG domain profile. / CITRIC ACID / DUF4176 domain-containing protein / LXG domain-containing protein
Function and homology information
Biological speciesStreptococcus intermedius B196 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGarrett, S.R. / Kim, Y. / Whitney, J.C.
Funding support Canada, European Union, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173486 Canada
European Molecular Biology Organization (EMBO)ALTF 139-2024European Union
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: A widespread family of molecular chaperones promotes the intracellular stability of type VIIb secretion system-exported toxins.
Authors: Gkragkopoulou, P. / Garrett, S.R. / Shah, P.Y. / Grebenc, D.W. / Klein, T.A. / Kim, Y. / Whitney, J.C.
History
DepositionDec 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4176 domain-containing protein
B: DUF4176 domain-containing protein
C: DUF4176 domain-containing protein
D: DUF4176 domain-containing protein
E: LXG domain-containing protein
F: LXG domain-containing protein
G: LXG domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2428
Polymers123,0507
Non-polymers1921
Water4,071226
1
A: DUF4176 domain-containing protein
B: DUF4176 domain-containing protein
E: LXG domain-containing protein
F: LXG domain-containing protein


Theoretical massNumber of molelcules
Total (without water)65,1264
Polymers65,1264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-57 kcal/mol
Surface area20590 Å2
MethodPISA
2
C: DUF4176 domain-containing protein
D: DUF4176 domain-containing protein
G: LXG domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1154
Polymers57,9233
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-47 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.822, 54.855, 119.922
Angle α, β, γ (deg.)99.943, 96.421, 90.785
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
DUF4176 domain-containing protein


Mass: 25360.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius B196 (bacteria)
Gene: SIR_0168 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZCF9
#2: Protein LXG domain-containing protein


Mass: 7203.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius B196 (bacteria)
Gene: SIR_0169 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZCZ9
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium tartrate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.94→30.87 Å / Num. obs: 68651 / % possible obs: 97.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.063 / Rrim(I) all: 0.09 / Net I/σ(I): 8.2
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9922 / CC1/2: 0.5 / Rpim(I) all: 0.824 / Rrim(I) all: 1.165 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
AutoProcessdata reduction
Aimlessdata scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→30.87 Å / SU ML: 0.3035 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.3279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 3280 4.78 %
Rwork0.2044 65331 -
obs0.2062 68611 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.97 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 13 226 7910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318022
X-RAY DIFFRACTIONf_angle_d0.600410905
X-RAY DIFFRACTIONf_chiral_restr0.0441227
X-RAY DIFFRACTIONf_plane_restr0.0041396
X-RAY DIFFRACTIONf_dihedral_angle_d14.25212994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.36791450.34142823X-RAY DIFFRACTION96.49
1.97-20.35551520.33812800X-RAY DIFFRACTION96.82
2-2.030.33221510.30262799X-RAY DIFFRACTION96.98
2.03-2.060.32681510.29442780X-RAY DIFFRACTION96.76
2.06-2.10.32961480.28422875X-RAY DIFFRACTION97.39
2.1-2.140.30831590.26972737X-RAY DIFFRACTION97.15
2.14-2.190.34021450.26182831X-RAY DIFFRACTION97.06
2.19-2.230.29411210.25622868X-RAY DIFFRACTION97.46
2.23-2.290.28621390.24972821X-RAY DIFFRACTION97.69
2.29-2.340.2961190.22852838X-RAY DIFFRACTION97.27
2.34-2.410.26331320.22722845X-RAY DIFFRACTION97.93
2.41-2.480.25271330.22592867X-RAY DIFFRACTION97.69
2.48-2.560.26441210.2252850X-RAY DIFFRACTION98.02
2.56-2.650.27941410.23782852X-RAY DIFFRACTION97.84
2.65-2.750.31191270.23982883X-RAY DIFFRACTION98.3
2.75-2.880.28821240.23532859X-RAY DIFFRACTION97.93
2.88-3.030.28261380.22522843X-RAY DIFFRACTION98.55
3.03-3.220.27931860.22262831X-RAY DIFFRACTION98.5
3.22-3.470.22171470.20072867X-RAY DIFFRACTION98.75
3.47-3.820.23611630.18832833X-RAY DIFFRACTION98.85
3.82-4.370.18921700.15732829X-RAY DIFFRACTION99.07
4.37-5.50.18221390.15312924X-RAY DIFFRACTION99.32
5.5-30.870.17791290.16322876X-RAY DIFFRACTION99.24
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)
18.714037410761.78542946108-1.536557817143.003099052750.7292830210937.513751749110.08643788899830.5053120556280.106685752685-1.74503304716-0.431602563348-0.498374217991-1.639001429340.5204792058510.0620740389390.772567344085-0.1107439947020.01413481298950.8105391193050.006108530848020.39273810750318.22155897937.708234637141.39678198301
24.27046615314-0.5626824007930.9609894608516.20500246284-0.1154125842431.740812335640.3652881500270.216462239250.356062651899-0.4337568107720.0556332174959-0.70779235563-0.3506400751210.298484162317-0.3099995615210.701792160545-0.2000949039680.1154394273720.386037718453-0.0206644908270.36635954240817.857419699215.255791610113.954015962
33.8785476118-1.645239970170.4445054294480.7517825616410.03845034314763.18495212252-0.1634063595460.4823665389040.566918898697-0.2912512366320.400791759164-1.013493785160.1605526284551.210909182960.2172847900431.50515759921-0.2966483928340.1438022039160.413341917431-0.2004936796441.0221130611220.027036387223.251298934717.2213700123
42.563653718080.0479568701124-1.738972921021.11006554835-0.03768462049583.280847979780.3453530073680.2421283488790.367183736781-0.190012889688-0.1564975315630.149948801045-1.17983022464-0.0181940377034-0.1026186228260.614250559642-0.0611634388161-0.03769581240310.2819304028260.03054731851060.3132761081655.6114833092112.399482256819.1533889648
52.01899606632-0.0285578995841-1.714013076961.693902381990.3621598086124.785664213270.1336111270480.186679769457-0.0361345099765-0.320391214834-0.09652237324240.0831246112739-0.508178442226-0.1047142087330.01173189947480.34730889517-0.0235876485239-0.04132052353270.247057565676-0.01651284096720.2984491180658.266248961132.2158740125815.7786872027
62.198550390510.777547843043-1.844887010073.06178951669-4.800216722027.743034697610.345637244965-0.5253209339930.3010903077470.982057584382-0.3069343668850.376427324336-0.750600067669-0.06946868007180.008212619117880.5787309000170.006600032718950.1197969111060.5550036786460.006057968894090.489673220825-7.75812155081-12.784607263558.9686685879
76.256594821691.58715859449-2.924110667065.19759250602-1.163155150899.39677634580.280643337568-0.4967083472840.549648990520.6815377599750.1230654974840.1147762966270.194057789914-0.194521913898-0.03449288079780.6256060355460.002362913161380.03215629786830.343254709472-0.03506552827110.319633128694-1.05334673344-18.892643521759.1988598167
84.002322642780.04318934372290.9685083640355.521485836610.1441864138638.42825140699-0.506594948933-0.1411640293730.0475034264397-0.5639309611050.320929898822-0.6604739909680.5596232772660.8006246839950.0261304566590.498200710498-0.008688519507170.2002568622290.414438774882-0.005939412927950.4978383655292.76273091556-22.13283710943.3369235061
93.03554929909-0.451266845936-0.3883798270335.50327309981-0.07480307841147.90843616591-0.262728831847-0.348891668289-0.5890317816630.2007523305720.0218859742303-0.4417509689561.30927718380.3959444471520.1680809865370.6526758995560.04526720850120.1477419403580.4259424324740.0418843265060.549910057675-0.422009018897-30.185423627252.2495901372
101.135397395131.74828591419-1.020398424783.95291672666-1.635611159653.897345002290.0296704603645-0.0429045229438-0.2339255782880.343675245544-0.08340700216090.4795236642960.61576284547-0.4635649204070.03866151642580.484350662987-0.09955897058810.1421596205310.3708910660690.03830203770440.41974341365-7.73733695669-21.334403806852.2627595511
111.836764916620.437559707223-1.166048554083.48104106451-1.395370310784.70706182245-0.265045768959-0.0832050048729-0.477376929346-0.182839351739-0.07506924229110.04995588438250.9336740269920.1398117781470.2439686933640.385992198642-0.02658014697730.06195461170430.3388330083780.009938523086040.3801806774184.08794534592-14.188938484234.3177159123
120.140516199875-0.4771992498570.388686473687.289884669682.750668020913.201105825870.3046205001620.355465654243-0.606168130334-1.25788429388-0.086327946588-0.0152031799050.395403558068-0.529324196996-0.06842676358350.59331576536-0.07802931499740.01807135886990.423044613652-0.1070464103450.6046863733943.15325980484-17.690213874322.8366816675
131.924626153650.0986473939079-1.391555364063.5131445888-0.4725559748725.3328192984-0.1468076524040.0696858161578-0.1758269133490.2392430812930.07529007987060.3554651035910.0522546397097-0.3532199263480.06398958457280.20991359563-0.047446109173-0.009456734676430.3030576118930.03124357226430.334891401481-2.77902663334-7.4736668856236.2991192836
145.055289558840.77553616942-1.680507676741.27124135447-1.557383223892.35184847632-0.0256391610750.412257026868-0.553592899439-0.2470432821360.3725636622490.7732495533350.38811537218-0.6773209696640.1062238676350.321045702171-0.09157955054280.1346445983810.4823851093040.02326119476930.575733176302-12.5030407495-14.610056451944.100669563
153.590563031362.692864149650.8838058234995.663902180012.635433773951.87317019984-0.108392857489-0.39913608413-0.03726474957810.4752435710240.0743406926681-0.115354364460.2807499822580.3633980268160.1225254637750.4623999879360.2083294652140.006721205602550.4510908753130.02197342817280.29727591384713.0550121712-12.0909394052-9.23357779272
166.434965689522.61552764638-0.2987463292112.817379430880.04101036967131.571446180760.1062907635720.0626418449953-1.187598587990.368088165164-0.104171389687-0.1647742760840.2316841619140.5472440949840.124074987070.7889153717710.1829972281860.02423958578660.5657171079890.01486917346340.50583612866814.4838674761-24.18801656-15.9042344933
173.37189379023.562148199671.722249941354.366187498950.3072666167214.809882588760.642549201197-1.00228787662-1.811219955260.551999237327-0.549817365425-0.6304878913260.7888388923750.37024145997-0.09470358739190.9130893150290.2778638384460.06706657981990.4921782542440.1355161496290.53729424739912.3180507589-25.8423537419-7.32542846474
181.40285396227-0.2953961798980.7553005577280.9540042730180.1737024482521.47723443803-0.0371512001789-0.0812411607745-0.204168996230.08572282604530.04143397355340.1184115908680.5945679247160.108565581786-0.01363314061540.4245395555250.07599082171510.06716471573760.2845133414830.004291202474560.2658768232470.767000303854-11.9351914491-21.8994688569
196.02390285666-1.456758426390.7809323962517.202799392080.469246403317.64915922361-0.0291536906644-0.274954671994-0.3811329799520.248287507948-0.0954122398571.084420196740.350006285393-1.346013350660.01363031745260.4070561286390.05157822362780.01328399925170.578484951415-0.07070973134410.406062038888-5.37932863736-3.47826469852-11.268400344
202.793333534530.5238210663780.8914194056844.30298854178-0.3742473565222.46266422986-0.0715307595838-0.109664216958-0.1102790639130.1362522920620.0862841536-0.02941979760630.3837546339420.251451872795-0.008499202966090.2515441533520.05404593124830.02129428474830.278853306681-0.01962890498090.247915209033-2.59803805421-3.69060658978-28.1841646995
214.910827739754.53085961452-3.252087638818.08422006419-4.529105806432.81791985828-0.0194906140995-0.334312929520.4637800292330.8331290625560.106960419838-0.667738108303-0.551889882139-0.232583387586-0.08660839612270.4335691669470.0696490439128-0.06477945562660.363238559119-0.07608960339350.4662842418137.485667095676.51414708855-15.1212035428
224.79149961956-0.00657114403589-0.8581673642840.922955127677-1.998395905234.67021465215-0.380977045137-0.8348699275470.1084663989390.3027573275550.03219577974670.09779481135040.468641938454-0.08803081680140.1884281165360.4551908603950.1238565168570.04649922561220.386112452097-0.05380421049490.2810115631871.15794266731-5.30234690609-8.10524647233
232.39045884474-3.042907803122.874619424044.12178606074-4.244931422414.577813065980.491758215770.0322684612181-0.52243658548-1.038492211970.05649473296290.6144202264171.06252138775-0.260781150995-0.5383820071040.671138830568-0.0724240474992-0.1545303386790.589076415490.06622115269950.481319222496-13.222495818412.9522580602-59.2959963715
242.748714657160.3692499521130.668148286934.80798108750.4944054036396.91051305507-0.1553089620430.192588662660.212642810915-0.4839510729960.0346626307004-0.317600408863-0.8774622994620.2803983928710.08166290782390.437749931684-0.0246411239549-0.02998527171010.2999291241830.003939400080770.369605062368-5.8963731489626.1279864343-52.0347779309
250.900342764297-0.9207851217280.744988778642.69914586732-1.353790018864.39012689117-0.162820055375-0.08361198421290.2430890079540.1468571934150.05661239630480.0471923619947-0.401999672958-0.1644863166630.1689324290060.1987964914530.0314335460905-0.037995037160.255086356826-0.02681068418580.3489759777-6.8996712469314.4946530557-35.1318286222
260.5404343716690.1814684209930.3570551139373.57809892673-0.9925336550053.040008313730.003523053798940.05877136183720.0216624073412-0.592292302252-0.02752029254430.6264753433550.0396126867693-0.409975895228-0.002021774976090.411876304480.0234580840269-0.08713373497810.325349938018-0.01525009234640.340508651317-12.49112623136.98604661869-45.6777500541
275.52186913896-0.3378225619870.3729476293345.63387051803-3.511046436089.541566746980.3512252281240.5018043048030.284568496306-0.07860624851140.3543947993640.909199941195-0.732336325768-0.816201405176-0.5137442180720.3033177968130.0606458812296-0.02907697906760.369205690540.0216281568930.458229443438-9.497932107428.5779120812926.8452837465
285.25070557956-1.15839187245-2.460731008981.65441481225-0.002120695039186.60583510969-0.4080819489860.808956447675-1.10732273657-0.4689489772250.3729891263441.155812800491.18378480431-1.87370800697-0.1614272617790.634155508998-0.205127088885-0.2854982069480.721388578986-0.04267435312040.95531301003-14.3322445184-7.7099926050525.3868740535
293.8814024229-0.1835722658122.804840386665.879044989341.894234486354.836657902140.01867564658710.9401550858080.0435786562238-0.4051939982661.455067688910.4679154086030.61624674465-1.64344365714-1.08351928571.04307991622-0.362079258837-0.132773502231.34350987162-0.2275709248441.00119547902-3.60956084132-14.703800889317.5616842048
302.61046005109-0.1249485863280.515473999124.65879889428-3.872708749497.8548426579-0.07475815803020.0583004656368-0.0209246407442-0.3813457712310.4512219761260.4367227445060.638827882988-0.536798590127-0.5140835177190.341128936893-0.07485375181270.001107982804250.341907003964-0.01297153366030.367463244806-14.5368084692-9.22890085526-30.7550348699
318.9560559776-0.238820348083-0.4083529864624.714718254690.3341415767578.75527081423-0.452272155402-0.830575062412-0.5315189034390.9812055886380.8529208265690.248872112181-0.00874629757558-0.537578433706-0.45643839560.4406997911640.07393959598010.1715111987820.5031230809660.06293793505130.558161694791-13.0795773127-6.88255692644-15.8346332501
321.11850769245-0.459507610420.9531799485362.419207917851.476558198433.01992325238-0.312413592663-0.6134255290580.6818734736480.7523160226210.7162311678111.89252403821-0.251139619049-1.6362759963-0.005290407760210.4144249223370.1972427199640.2842535762890.5014818444020.1253038208080.91311366091-19.10477625957.57392197713-24.8081834208
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 18 )AA2 - 181 - 17
22chain 'A' and (resid 19 through 47 )AA19 - 4718 - 46
33chain 'A' and (resid 48 through 63 )AA48 - 6347 - 62
44chain 'A' and (resid 64 through 169 )AA64 - 16963 - 168
55chain 'A' and (resid 170 through 215 )AA170 - 215169 - 214
66chain 'B' and (resid 3 through 18 )BB3 - 181 - 16
77chain 'B' and (resid 19 through 34 )BB19 - 3417 - 32
88chain 'B' and (resid 35 through 47 )BB35 - 4733 - 45
99chain 'B' and (resid 48 through 80 )BB48 - 8046 - 78
1010chain 'B' and (resid 81 through 101 )BB81 - 10179 - 99
1111chain 'B' and (resid 102 through 117 )BB102 - 117100 - 115
1212chain 'B' and (resid 118 through 140 )BB118 - 140116 - 138
1313chain 'B' and (resid 141 through 204 )BB141 - 204139 - 202
1414chain 'B' and (resid 205 through 215 )BB205 - 215203 - 213
1515chain 'C' and (resid 2 through 47 )CC2 - 471 - 46
1616chain 'C' and (resid 48 through 68 )CC48 - 6847 - 67
1717chain 'C' and (resid 69 through 81 )CC69 - 8168 - 80
1818chain 'C' and (resid 82 through 140 )CC82 - 14081 - 139
1919chain 'C' and (resid 141 through 153 )CC141 - 153140 - 152
2020chain 'C' and (resid 154 through 187 )CC154 - 187153 - 186
2121chain 'C' and (resid 188 through 198 )CC188 - 198187 - 197
2222chain 'C' and (resid 199 through 215 )CC199 - 215198 - 214
2323chain 'D' and (resid 2 through 18 )DD2 - 181 - 17
2424chain 'D' and (resid 19 through 80 )DD19 - 8018 - 79
2525chain 'D' and (resid 81 through 187 )DD81 - 18780 - 186
2626chain 'D' and (resid 188 through 215 )DD - E188 - 301187
2727chain 'E' and (resid 2 through 25 )EF2 - 251 - 24
2828chain 'E' and (resid 26 through 38 )EF26 - 3825 - 37
2929chain 'F' and (resid 2 through 17 )FG2 - 171 - 16
3030chain 'G' and (resid 2 through 19 )GH2 - 191 - 18
3131chain 'G' and (resid 20 through 24 )GH20 - 2419 - 23
3232chain 'G' and (resid 25 through 38 )GH25 - 3824 - 37

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