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- PDB-8pxt: Targeting extended blood antigens by Akkermansia muciniphila enzy... -

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Basic information

Entry
Database: PDB / ID: 8pxt
TitleTargeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / Beta-hexosaminidase / Akkermansia muciniphila / GalNAc-B converting / CBM
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / lysosome / carbohydrate metabolic process / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJensen, M. / Abou Hachem, M. / Morth, J.P.
Funding support1items
OrganizationGrant numberCountry
Other government0136-00086A
Citation
Journal: Nat Microbiol / Year: 2024
Title: Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood.
Authors: Jensen, M. / Stenfelt, L. / Ricci Hagman, J. / Pichler, M.J. / Weikum, J. / Nielsen, T.S. / Hult, A. / Morth, J.P. / Olsson, M.L. / Abou Hachem, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year
Revision 1.2May 15, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,42915
Polymers219,7533
Non-polymers1,67612
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint2 kcal/mol
Surface area72970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.230, 169.060, 171.970
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

#1: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 73250.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Mutation to the catalytic acid E339A (321 in the sequence)
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_0369 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UN02
#2: Sugar
ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 11% PEG8000, 0.5 M NaCl, 0.1M NaCacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.25→62.32 Å / Num. obs: 127867 / % possible obs: 99.96 % / Redundancy: 11.3 % / Biso Wilson estimate: 47.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.038 / Rrim(I) all: 0.129 / Net I/σ(I): 12.86
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 12605 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→62.32 Å / SU ML: 0.3186 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2102 6403 5.01 %
Rwork0.1798 121440 -
obs0.1813 127843 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.39 Å2
Refinement stepCycle: LAST / Resolution: 2.25→62.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15036 0 110 521 15667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315521
X-RAY DIFFRACTIONf_angle_d0.640121017
X-RAY DIFFRACTIONf_chiral_restr0.04632272
X-RAY DIFFRACTIONf_plane_restr0.00592703
X-RAY DIFFRACTIONf_dihedral_angle_d13.76735689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.38411950.3323990X-RAY DIFFRACTION99.98
2.28-2.30.3032030.30034035X-RAY DIFFRACTION100
2.3-2.330.35352280.28483954X-RAY DIFFRACTION100
2.33-2.360.28791990.26654037X-RAY DIFFRACTION99.98
2.36-2.390.31162360.25623973X-RAY DIFFRACTION100
2.39-2.420.27572050.2394039X-RAY DIFFRACTION100
2.42-2.460.27081880.22334015X-RAY DIFFRACTION100
2.46-2.50.2691980.21454060X-RAY DIFFRACTION100
2.5-2.530.22532210.20543973X-RAY DIFFRACTION100
2.53-2.580.26922220.19944007X-RAY DIFFRACTION100
2.58-2.620.26862090.20344006X-RAY DIFFRACTION99.98
2.62-2.670.25212170.2083989X-RAY DIFFRACTION99.95
2.67-2.720.25362320.20954047X-RAY DIFFRACTION99.93
2.72-2.770.24271630.21824056X-RAY DIFFRACTION100
2.77-2.830.25832080.23364035X-RAY DIFFRACTION99.98
2.83-2.90.28512090.24584012X-RAY DIFFRACTION99.93
2.9-2.970.28011990.22724085X-RAY DIFFRACTION100
2.97-3.050.25671880.20964017X-RAY DIFFRACTION100
3.05-3.140.23122330.18764029X-RAY DIFFRACTION100
3.14-3.240.1972550.18973989X-RAY DIFFRACTION100
3.25-3.360.212130.18774044X-RAY DIFFRACTION100
3.36-3.50.23572200.18664050X-RAY DIFFRACTION99.98
3.5-3.650.20382080.16734069X-RAY DIFFRACTION100
3.65-3.850.18972300.15184070X-RAY DIFFRACTION100
3.85-4.090.18052210.14514046X-RAY DIFFRACTION100
4.09-4.40.14862200.13414092X-RAY DIFFRACTION99.98
4.4-4.850.15852080.12814124X-RAY DIFFRACTION100
4.85-5.550.16982400.13734087X-RAY DIFFRACTION100
5.55-6.990.20252190.17014172X-RAY DIFFRACTION99.98
6.99-62.320.18112160.17944338X-RAY DIFFRACTION99.45
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)
10.3313715721990.0280012476-0.3314630030270.474185779101-0.08901458639940.646187664597-0.5399676519530.403452825171-0.71718470732-0.6979321999860.223497739655-0.2549656967390.886020753555-0.270061028187-0.03299987130911.01287665282-0.2102857681910.2580789242430.599536431125-0.1808638240160.84402521975212.656138564-17.77811636716.7401730075
20.6695885397870.0984055238574-0.382186374440.195755014371-0.09681636598740.284340547132-0.2535010436080.236195447622-0.595014748556-0.8170165602750.1139208963460.1248786652870.711230376721-0.455920816424-8.15353576075E-51.05630522807-0.3375398523430.08283527025830.885199761862-0.1871173882170.7518948072334.00250194251-16.584207136910.5980839899
31.429267892770.20976882827-0.3379837940121.8345337592-0.3625986424571.3194574295-0.1425337297520.3011516564380.133632137138-0.1514199300430.1316970134470.2943330854370.00140520437938-0.3838839870781.47644936565E-50.401597323666-0.047953062114-0.05249138475530.5950749418060.03792795072450.4620125158852.388507679814.677560621521.0262480266
40.4097176221450.240058528551-0.5030360232510.986863752159-0.5487461316630.6860148872130.251391321719-0.1381286609670.2636108552630.5276956183670.1273276157740.447048471217-0.308499644944-0.286678744073-0.0001510892019870.5330486315140.02220012775940.05237802350730.553489712991-0.007301476568440.534761566082-0.76550240032714.386685312738.8356045413
51.237567904560.228950074168-0.3653208017951.428164359690.1194442973510.777478479302-0.0627535586068-0.0306875966357-0.02252558850540.07053583510990.0474810670534-0.008682550140120.108163508604-0.00696841876755-2.2686510194E-60.352919038591-0.0163588146198-0.02195914788970.455882664053-0.008492498158230.40703793747213.22363584878.3044742564330.9340456827
60.665892259411-0.04952367943230.4938231044780.0317947755835-0.06143871961370.433365944779-0.2539272130250.0507731981414-0.166928370153-0.0238903743970.0522846194032-0.1017429817710.0944360497523-0.067611675459-2.94409163122E-50.5374895432050.03644285531450.04173510643530.5929343119320.006031773077590.6018765978628.0497827270.6354683797726.4026268496
71.53126503636-0.7936446860420.4179949979761.39093670443-0.1888045720632.018905507480.04350068971750.01091262701280.1010982026960.02192643195920.0418977691949-0.138037731247-0.131536834406-0.0273134491739-1.00640247105E-50.5294467885390.0912250800222-0.04749744641430.455649003843-0.03600438049910.55036455144945.9395803946-4.5659910773237.4652900527
80.392880066191-0.1588628006560.4449334676980.480594405658-0.1419987385640.5245239256170.1749003415980.577773791446-0.107642324042-1.05257441436-0.3454953916310.548271288118-0.0400741574477-0.187963225575-0.2565290483681.86874932010.433271684455-0.4259349993370.839162623965-0.07493212743540.48533876046145.1149385918-34.5222730824-0.00743305613918
90.81499192257-0.1485616083370.2015345914420.312665249111-0.5346175028060.9027011940090.05584314318340.320482771924-0.507614714455-0.783764729875-0.2065440565350.4463333055460.192627023811-0.174126227398-0.08314242379621.591056292160.354667816662-0.5280929732170.730972331289-0.236015312060.6708881699741.1527624056-39.89871169993.83638453682
100.980784218328-0.4895329944950.2590780319742.2919009589-0.2303976704451.549649944180.168026320622-0.0188719974861-0.207403142281-0.546500858037-0.1514856644520.45416705470.160991290232-0.300007439942-0.06949053007060.5217502304350.0168334213291-0.1467248602650.39897106061-0.03895684279940.56578194180947.6796574059-43.733883937533.907937947
111.0634203771-0.5575297829540.2142113361011.05543792675-0.4355273000271.469075241790.08932152846240.000160980793037-0.118495638876-0.352609204416-0.06141446721220.08689315741310.38755708350.100094914581.86275527564E-60.5720852804660.0309423796159-0.04886346208960.3881543162690.01589448051860.56913411799662.0679926402-56.276517154542.3434086113
120.6044308754-0.429631669463-0.3209160192930.651112135881-0.3052133500080.9560950138960.02874895790330.2149719867970.0964892490899-0.277518853402-0.104020762758-0.3695653151280.1201152827680.594933629898.51610943203E-50.7418806738580.0817180005520.01447931790660.555214829349-0.00409769252620.57170532136168.4956625909-49.703600802630.1508159765
130.9205867489130.3068226327480.9718428558612.49371920215-0.75531414712.054420667070.1555067297220.177680184890.0863001231399-0.854261846845-0.220547911807-0.0732012187037-0.04838343374920.313748904528-2.93696590486E-50.7112786190310.0657690061838-0.01593020380980.3877802614170.01376177718150.4439835971860.1679321057-34.716079116625.5819293126
140.06765862239790.253776479299-0.04074811666340.8086553983710.02837025630350.5782279364020.140629871596-0.101501370644-0.136973227121-0.40964861794-0.247646550634-0.08535803293250.3870798159280.3529485810192.69399909102E-50.8344469233050.130111561905-0.1194376636570.584365070662-0.00113936091230.56026554673355.3414767871-18.852346922118.3100302821
151.67099308535-0.2317684991260.6107621985571.81741474982-0.07492810300541.292547979590.0572271624061-0.4235433644310.07394801074340.0764935214855-0.0776765808582-0.0530978243290.04999797297610.315785691827-2.47754016573E-50.427972658651-0.0240725199208-0.02308481654760.736380526701-0.0005274293711150.500277530464.6892782560.68024202165812.8607416493
160.4817056218440.143328141349-0.1677588932170.670973985179-0.291319167950.1763737996150.0841814860112-0.02688592188330.0839068384920.413620339717-0.02432204879570.2851252841820.207309058979-0.459818869054-3.30670119527E-50.519536717544-0.07287129469830.08453591686010.6861430544310.004952196558310.56342364806226.6243507989-3.52680300314-15.6775439926
170.954913037168-0.05916670581230.3831595899430.617033753804-0.3313771108190.7571498216180.03869491378640.346619400851-0.085386110231-0.102409909207-0.1169097568140.1370458185070.243285334943-0.250918820077-1.29068441885E-50.568885070711-0.1012256733110.03442610132420.69074234612-0.04748328937570.5485353200427.8128934218-9.48017260037-24.968232009
181.364620393030.770503168488-0.08071765434431.018890815320.5927989538640.9670790304690.0996932345515-0.0339221831719-0.200905040880.171492398735-0.1012831809660.2352495682570.390459306524-0.0710789260882-1.06201173909E-50.465665193588-0.02046238479980.05291011475360.5897665484140.02473552908450.53699326122833.2504662116-5.02483079171-17.8647505094
192.168159241560.489760405992-0.9216849995340.758479740834-0.09626576406971.19030188764-0.00445878822188-0.00137885580468-0.1488513190770.0103024059966-0.00584308227976-0.09405468497390.05477276712420.03057606424139.24164195316E-60.4123653959320.02460460110840.008386346020730.402147967440.0272730407470.39512626821160.09481107582.7677814404-26.1348065947
201.139390495250.397703536641-1.13716889921.46027438137-0.3674549208451.182007185420.06156700475180.1372182312480.153418332776-0.1820259557530.0233645762305-0.0058014245432-0.107557866789-0.124943651581-1.37835806896E-50.4649181957330.05129990410120.008919963624970.4504009624240.03578219035860.42927065890466.309525190517.6624347723-39.3960195208
211.86597663290.591157638755-0.2535864724041.2377756443-0.4688055471421.874525703270.103904336886-0.1173303421690.3174484012960.170583555647-0.01003173560840.15528698271-0.265785021543-0.111669686632-3.41566179578E-50.4174385417080.0404722019910.04067300581120.421174280188-0.01189105004580.44979686516150.259216295114.6612543559-19.3644786962
220.627026839994-0.240585453179-0.4846733333530.1980676950860.05230802964270.4659851575890.14678592699-0.03917219573690.522123106183-0.3475850204580.366111425652-0.554662594136-0.6143424728690.27772124651-9.31923757254E-60.6716710806830.01122054061870.05293379061590.7309471194120.003700766099030.72662147426450.140593665816.9628470545.43077041276
231.34442625088-1.39476927004-0.8276518217241.803842287150.7547413387861.11191083383-0.0703277558163-0.09363110758260.472557270469-0.01793733509550.256596638372-0.541407681372-0.2182360500880.1802305555885.56538946752E-50.482113527116-0.04381900562070.04961182791060.654535198635-0.01420166670780.68864377940543.345894496619.572756806415.5894103931
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 34 )AA2 - 341 - 33
22chain 'A' and (resid 35 through 82 )AA35 - 8234 - 81
33chain 'A' and (resid 83 through 364 )AA83 - 36482 - 363
44chain 'A' and (resid 365 through 412 )AA365 - 412364 - 401
55chain 'A' and (resid 413 through 498 )AA413 - 498402 - 487
66chain 'A' and (resid 499 through 542 )AA499 - 542488 - 531
77chain 'A' and (resid 543 through 647 )AA543 - 647532 - 636
88chain 'B' and (resid 2 through 34 )BE2 - 341 - 33
99chain 'B' and (resid 35 through 130 )BE35 - 13034 - 129
1010chain 'B' and (resid 131 through 292 )BE131 - 292130 - 291
1111chain 'B' and (resid 293 through 364 )BE293 - 364292 - 363
1212chain 'B' and (resid 365 through 412 )BE365 - 412364 - 400
1313chain 'B' and (resid 413 through 498 )BE413 - 498401 - 486
1414chain 'B' and (resid 499 through 542 )BE499 - 542487 - 530
1515chain 'B' and (resid 543 through 647 )BE543 - 647531 - 635
1616chain 'C' and (resid 2 through 34 )CH2 - 341 - 33
1717chain 'C' and (resid 35 through 82 )CH35 - 8234 - 81
1818chain 'C' and (resid 83 through 130 )CH83 - 13082 - 129
1919chain 'C' and (resid 131 through 292 )CH131 - 292130 - 291
2020chain 'C' and (resid 293 through 364 )CH293 - 364292 - 363
2121chain 'C' and (resid 365 through 515 )CH365 - 515364 - 502
2222chain 'C' and (resid 516 through 550 )CH516 - 550503 - 537
2323chain 'C' and (resid 551 through 647 )CH551 - 647538 - 634

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