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- PDB-8fsd: P130R mutant of soybean SHMT8 in complex with PLP-glycine and for... -

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Basic information

Entry
Database: PDB / ID: 8fsd
TitleP130R mutant of soybean SHMT8 in complex with PLP-glycine and formylTHF
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / Enzyme / complex / mutant / substrate analog
Function / homology
Function and homology information


purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity ...purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-FFO / Chem-PLG / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsBeamer, L.J. / Korasick, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 2152548 United States
Citation
Journal: Febs J. / Year: 2024
Title: Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance.
Authors: Korasick, D.A. / Owuocha, L.F. / Kandoth, P.K. / Tanner, J.J. / Mitchum, M.G. / Beamer, L.J.
#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
DepositionJan 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,98638
Polymers216,2534
Non-polymers4,73234
Water36,3362017
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)86.565, 90.480, 146.183
Angle α, β, γ (deg.)90.000, 90.395, 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
Serine hydroxymethyltransferase


Mass: 54063.289 Da / Num. of mol.: 4 / Mutation: P130R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 100305380 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0R0IK90
#2: Chemical
ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23N7O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2017 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.18-0.25 TMAO 0.1 M TRIS HCL 21-23% W/V PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→47.64 Å / Num. obs: 361249 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.052 / Rrim(I) all: 0.099 / Χ2: 0.8 / Net I/σ(I): 7
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.464 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 16711 / CC1/2: 0.336 / Rpim(I) all: 0.968 / Rrim(I) all: 1.764 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→47.41 Å / SU ML: 0.2052 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 17758 4.97 %
Rwork0.1842 339672 -
obs0.1857 357430 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.15 Å2
Refinement stepCycle: LAST / Resolution: 1.49→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14422 0 320 2017 16759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006315656
X-RAY DIFFRACTIONf_angle_d1.017821272
X-RAY DIFFRACTIONf_chiral_restr0.08092276
X-RAY DIFFRACTIONf_plane_restr0.00732778
X-RAY DIFFRACTIONf_dihedral_angle_d8.41812272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.38394450.3558149X-RAY DIFFRACTION70.38
1.51-1.520.35875200.341210378X-RAY DIFFRACTION89.82
1.52-1.540.32936260.313711364X-RAY DIFFRACTION98.38
1.54-1.560.33166280.302211534X-RAY DIFFRACTION99.71
1.56-1.580.30735930.285411597X-RAY DIFFRACTION99.9
1.58-1.610.31365910.275411563X-RAY DIFFRACTION99.96
1.61-1.630.28695040.261111699X-RAY DIFFRACTION99.96
1.63-1.650.27575190.249211631X-RAY DIFFRACTION99.98
1.65-1.680.27635730.247611654X-RAY DIFFRACTION99.95
1.68-1.710.26465640.234711617X-RAY DIFFRACTION99.93
1.71-1.740.25746560.232111539X-RAY DIFFRACTION99.97
1.74-1.770.26846090.230211569X-RAY DIFFRACTION99.94
1.77-1.80.27495770.24111628X-RAY DIFFRACTION99.98
1.8-1.840.27066470.232111548X-RAY DIFFRACTION99.97
1.84-1.880.26276050.221411577X-RAY DIFFRACTION99.92
1.88-1.920.22986150.202411588X-RAY DIFFRACTION99.81
1.92-1.970.23156010.192911596X-RAY DIFFRACTION99.84
1.97-2.020.22215810.191811606X-RAY DIFFRACTION99.74
2.02-2.080.22095710.190411535X-RAY DIFFRACTION99.28
2.08-2.150.22336710.190411460X-RAY DIFFRACTION99.16
2.15-2.230.21596530.180811425X-RAY DIFFRACTION98.84
2.23-2.310.20356010.179211446X-RAY DIFFRACTION98.5
2.31-2.420.20956250.175911405X-RAY DIFFRACTION98.38
2.42-2.550.20756260.173811344X-RAY DIFFRACTION97.63
2.55-2.710.20535700.171811312X-RAY DIFFRACTION96.81
2.71-2.920.20485830.165811276X-RAY DIFFRACTION96.57
2.92-3.210.18515880.160111086X-RAY DIFFRACTION95.19
3.21-3.670.18485890.157411054X-RAY DIFFRACTION94.66
3.67-4.630.16816510.1411013X-RAY DIFFRACTION94.5
4.63-47.410.18555760.16211479X-RAY DIFFRACTION96.03
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)
11.016612307560.05259605090440.06284538149560.538375222488-0.08652658828661.04005428177-0.009447723466860.1101621165820.0851030931953-0.0972989704105-0.0335743778404-0.037346645753-0.2843226228540.1064663346510.04182838262490.2828191516320.007625296408850.02026577437070.156249904970.05269602516680.13122362808734.821371398935.13548751833.88775937812
20.975868855530.226353988496-0.09542248307190.730881879963-0.000129485927421.261724747990.02318901289210.08788617089740.0393383316972-0.077350567701-0.05171570437430.122934928494-0.176604562043-0.3230686693470.01700531566410.1734430538420.0856279794973-0.01241764673670.215088243862-0.01333979700110.1506628651367.7669838501328.836717212515.4201046234
32.502065599290.03791425371490.344201232382.674907392350.20543489131.69957491135-0.0308369397551-0.285062892710.2768200396180.203037602969-0.01912859725320.312036022459-0.283961173673-0.302615747740.02559663008760.2546730322430.0891518557160.00250230317890.1778664336830.001086286270120.1853314621513.479138605540.253937870118.2122142418
41.298183679940.06285962329950.05933691130080.4062247541660.1727638545780.8696143008340.001926147631570.2802744143710.0233128112872-0.206474123062-0.04385395301240.101233540811-0.325124185738-0.05990071258430.06720709286280.3054092303130.0872497681448-0.03639171494830.1648131595860.01566459494450.1673539559117.909074471736.30902508030.756706202783
52.66688751870.0576979935607-0.7109332983193.817422616991.0990384192.49211388908-0.1056160418150.164385338822-0.2694818960750.0859616893872-0.1853639225030.341240138520.166810449991-0.4523784556640.2619692487910.2463539617810.0327953229514-0.01672092641070.309884251842-0.05480227868590.1753981223959.755436624518.0992733103-8.59959592265
61.282177446520.6325818357621.336322215764.161564609782.603305912172.43816048673-0.03628041055470.195290036225-0.0409867734510.0650513276265-0.04378170069560.260950052890.0714485496280.1590000652620.08818191276020.3335170280180.1008749853440.06222470490720.320454209342-0.01363726220080.13940903634522.983344832918.0905191427-16.6399360204
71.76895159828-0.6038923462081.317379319141.30841170239-1.066551449763.33737875178-0.1213616970250.2498497224490.308018648498-0.096760601164-0.0214077133504-0.0147793985108-0.4530283358290.1525765612970.2037612844330.4228385174-0.01260293496260.02227408432290.1756980408640.08418403036940.1854727743433.249062421846.0134200097-1.1101698927
81.56480170340.2021298935270.8851583481130.209811337085-0.03177827664641.50156225189-0.01523458436260.11106030802-0.039979848289-0.138430857224-0.0361948321335-0.000597390493252-0.1350718204130.03808004828920.04506189874240.2064098700350.03880436012280.03984010453670.1482263437580.01754089962660.1135457453235.571046418523.41252214663.53814026569
91.0198625417-0.05816254398930.297851001270.557665072206-0.06567227251631.51683908004-0.00649167818231-0.110062867139-0.01389212130270.0202739583053-0.0354496918319-0.0204361527802-0.150638146889-0.03038566101880.04399484531940.1473791940140.001015492627340.009850265894050.132270591660.03284936594780.14570262010134.355898729120.685850018327.768129405
106.392842044492.22734838425-1.721360835982.52850922217-2.460196492424.185123871870.105352905872-0.246966107172-0.1749062054020.111506085336-0.135872897973-0.0853468606959-0.07342203341030.1242449076380.01841239109950.1084638230340.0131196232243-0.0002130696916420.08550370367790.01709454192370.1237565823641.212319350416.169891880635.1093617097
114.321000699630.95668300753-1.559574159784.32564267299-2.374162086694.0377409948-0.074491005113-0.0330248140492-0.2759833180420.0478126244985-0.0305075995525-0.2021122096820.04824261901590.1522381958330.1381777653150.1090486142970.004760520306730.0007316630161410.100604059074-0.007544360734960.11030552845344.946307871114.142996903925.5830981263
122.42089963368-0.1343696043520.617442763131.50263169370.4460941940781.974718115940.117688718457-0.100989779091-0.4560016332820.0256615543666-0.04918281879430.07027197364480.2334879390760.040858459899-0.01801893673310.1398141284850.0250047384840.009554231531380.1233754139970.02784975756170.16438627552937.015086679610.989655338117.8644627398
133.472657435491.468866710491.08499145961.579324179050.1718403456851.03609017858-0.01836345562520.0452632753643-0.144710537771-0.085725703478-0.0693042721866-0.217629144588-0.1228797910470.1746600035830.09293959214530.1874557151030.01247068475360.04214751015440.1564514886510.05068761293410.12183583925146.902838795326.24975178913.3935883515
141.695502606160.7065041265071.146233389374.255356297270.02852508870150.845370282199-0.00322337064797-0.2018924618140.2970265841180.679350308075-0.1521014812690.270749246933-0.4137127834130.1206872133450.1145775648660.405191010995-0.1019366764660.04624289139260.2194109061680.01386302591250.21384913107352.065289995741.17878997927.9725036409
150.82004773090.05203902268520.8085454233511.02080941228-0.2711481729651.09349859814-0.05330201025020.06752545218980.3590171042380.265029409864-0.1842340890690.103919644149-0.5259336960270.01273630715630.1644223881130.596874570976-0.1292856920850.0132406358120.2388366842480.07360292150380.39477521374749.935323678450.909913479716.1958440381
160.837967573234-0.01729796491520.1045565299520.384450815641-0.08865451806550.527255127872-0.0201121894683-0.100190326522-0.1772423826960.0563668750535-0.01070076595760.04412487586060.0384251088173-0.02212971493660.02649369175440.173245004678-0.0232907309960.04269365519430.1796703365440.02799817122940.238640969961-1.644749682481.321604364163.5064005985
171.058884271880.0130801677998-0.1589268680920.578324183197-0.1411878893770.8336839666340.002200871207720.230220669195-0.104695002463-0.0859253106037-0.01805890997160.08588535722310.0497971784434-0.1204359104550.01473295878360.124439216305-0.00455242241316-0.002242295601280.207091286291-0.05458149204050.171337273445-3.691528221977.7334118030334.1983110229
182.29195601086-0.134883336664-0.03931444580062.267651695280.3633634834532.614491501280.04281309719750.400049183118-0.285330028678-0.295472745109-0.0252764638915-0.06003013772820.158457806370.0741265574474-0.003834910050730.150507401341-0.01630333649610.006464407670360.150734559012-0.04623408808470.213851923721.60399001172-3.8291288727337.9685316572
191.6250920147-0.4252854800860.4028969857890.485612859072-0.2963638377420.630323728913-0.00589371530027-0.0104733299407-0.360823612033-0.02385647863860.01677635603150.1987047490.0831485910882-0.137770152089-0.01609946850460.128100627014-0.0232148364070.01669067731460.141603884801-0.04359033488810.232724592223-12.9608120091.0043139956349.3911751011
201.31406368471-0.7879925997830.1460387098621.94140248472-0.04198723734411.339937819810.01344535085740.09940498224190.0132956275875-0.0499538505539-0.03508210320450.0187194200506-0.101866492152-0.1077000323890.01589600766430.0989638400125-0.005380594674420.004193641116790.205463895948-0.01924566748280.190343245868-23.485760550218.568125481947.3866601893
212.28080803858-1.499828617220.6090150600912.31282821799-0.0910029245910.199247830415-0.0638936447495-0.290183331469-0.0742560973824-0.01402224076860.05973304216850.0370620075076-0.0438295062958-0.0721304037418-0.009526435895430.186311652672-0.01622311286840.05601939121480.289793554092-0.0443646664120.178837013228-24.505809068518.246609359962.9108647909
220.659677363466-0.01338836025920.02178808519550.392371283412-0.1366075218020.510844101562-0.0216247571923-0.0550766830564-0.08233698713410.0199786083396-0.0418021230691-0.0223944933548-0.008647245106950.06861222461490.06736208819710.108698291593-0.01557119541230.01508199456290.1203236031870.007502151026070.13393869177412.908200009312.215893719458.1529736394
231.07505804036-0.007079645859220.1969567552541.34233188803-0.9811860420911.38380675864-0.00117309570405-0.0694920197003-0.19045059313-0.125715476024-0.188435373572-0.2355619368960.2280210829550.2309010499360.1231252892740.1604689794180.02520442365880.06011785458290.1612864567090.0348578608630.18195466924319.50345529523.208265486666.6260330288
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 89 )AA0 - 891 - 90
22chain 'A' and (resid 90 through 230 )AA90 - 23091 - 231
33chain 'A' and (resid 231 through 283 )AA231 - 283232 - 284
44chain 'A' and (resid 284 through 331 )AA284 - 331285 - 332
55chain 'A' and (resid 332 through 426 )AA332 - 426333 - 427
66chain 'A' and (resid 427 through 471 )AA427 - 471428 - 472
77chain 'B' and (resid 0 through 31 )BB0 - 311 - 32
88chain 'B' and (resid 32 through 89 )BB32 - 8933 - 90
99chain 'B' and (resid 90 through 169 )BB90 - 16991 - 170
1010chain 'B' and (resid 170 through 197 )BB170 - 197171 - 198
1111chain 'B' and (resid 198 through 230 )BB198 - 230199 - 231
1212chain 'B' and (resid 231 through 283 )BB231 - 283232 - 284
1313chain 'B' and (resid 284 through 332 )BB284 - 332285 - 333
1414chain 'B' and (resid 333 through 426 )BB333 - 426334 - 423
1515chain 'B' and (resid 427 through 471 )BB427 - 471424 - 468
1616chain 'C' and (resid 0 through 89 )CC0 - 891 - 90
1717chain 'C' and (resid 90 through 230 )CC90 - 23091 - 231
1818chain 'C' and (resid 231 through 283 )CC231 - 283232 - 284
1919chain 'C' and (resid 284 through 332 )CC284 - 332285 - 333
2020chain 'C' and (resid 333 through 426 )CC333 - 426334 - 427
2121chain 'C' and (resid 427 through 471 )CC427 - 471428 - 472
2222chain 'D' and (resid 0 through 230 )DD0 - 2301 - 231
2323chain 'D' and (resid 231 through 471 )DD231 - 471232 - 469

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