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- PDB-8bz8: Crystal structure of the L. monocytogenes RmlT D198A variant in c... -

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Basic information

Entry
Database: PDB / ID: 8bz8
TitleCrystal structure of the L. monocytogenes RmlT D198A variant in complex with TDP-rhamnose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / D(-)-TARTARIC ACID / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Glycosyltransferase
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsCereija, T.B. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: To Be Published
Title: Crystal structure of the L. monocytogenes RmlT D198A variant in complex with TDP-rhamnose
Authors: Monteiro, R. / Cereija, T.B. / Morais-Cabral, J.H. / Cabanes, D.
History
DepositionDec 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
C: Glycosyltransferase
D: Glycosyltransferase
E: Glycosyltransferase
F: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)433,89428
Polymers429,5646
Non-polymers4,33022
Water12,124673
1
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5439
Polymers143,1882
Non-polymers1,3557
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-51 kcal/mol
Surface area52240 Å2
MethodPISA
2
C: Glycosyltransferase
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5088
Polymers143,1882
Non-polymers1,3206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-43 kcal/mol
Surface area52050 Å2
MethodPISA
3
E: Glycosyltransferase
F: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,84311
Polymers143,1882
Non-polymers1,6559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-54 kcal/mol
Surface area52080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.397, 292.381, 93.075
Angle α, β, γ (deg.)90.000, 100.498, 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

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glycosyltransferase /


Mass: 71593.922 Da / Num. of mol.: 6 / Mutation: D198A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: APD94_03445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A401AAP7

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Non-polymers , 5 types, 695 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H26N2O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 7.0 0.2 M Potassium sodium tartrate tetrahydrate 22.5% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979415 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979415 Å / Relative weight: 1
ReflectionResolution: 2.52→49.28 Å / Num. obs: 154021 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 54.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.046 / Rrim(I) all: 0.122 / Rsym value: 0.113 / Net I/σ(I): 12.9
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.394 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7618 / CC1/2: 0.568 / Rpim(I) all: 0.558 / Rrim(I) all: 1.503 / Rsym value: 1.394 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BZ4
Resolution: 2.52→45.76 Å / SU ML: 0.3571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.13
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 7584 4.93 %
Rwork0.1907 146342 -
obs0.1926 153926 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.35 Å2
Refinement stepCycle: LAST / Resolution: 2.52→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29239 0 271 673 30183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002330162
X-RAY DIFFRACTIONf_angle_d0.469640787
X-RAY DIFFRACTIONf_chiral_restr0.04324472
X-RAY DIFFRACTIONf_plane_restr0.00315216
X-RAY DIFFRACTIONf_dihedral_angle_d12.483811376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.550.32512640.31544799X-RAY DIFFRACTION100
2.55-2.580.32762480.29914930X-RAY DIFFRACTION100
2.58-2.610.33172560.29974811X-RAY DIFFRACTION100
2.61-2.640.31112670.28744890X-RAY DIFFRACTION100
2.64-2.680.33292660.27484858X-RAY DIFFRACTION100
2.68-2.710.30292370.26554868X-RAY DIFFRACTION100
2.71-2.750.3082730.26284860X-RAY DIFFRACTION99.98
2.75-2.790.30352400.25434870X-RAY DIFFRACTION100
2.79-2.840.28442480.26674915X-RAY DIFFRACTION99.96
2.84-2.880.32762570.27444858X-RAY DIFFRACTION100
2.88-2.930.362530.27814869X-RAY DIFFRACTION100
2.93-2.990.31212310.27244893X-RAY DIFFRACTION100
2.99-3.050.32272460.25224868X-RAY DIFFRACTION99.98
3.05-3.110.2592600.23414893X-RAY DIFFRACTION99.96
3.11-3.170.28082670.2244829X-RAY DIFFRACTION99.98
3.17-3.250.25492530.21424886X-RAY DIFFRACTION100
3.25-3.330.25842270.21344917X-RAY DIFFRACTION99.98
3.33-3.420.25242710.21124843X-RAY DIFFRACTION100
3.42-3.520.2382270.21224896X-RAY DIFFRACTION100
3.52-3.630.22612630.19934890X-RAY DIFFRACTION100
3.63-3.760.22682730.17764849X-RAY DIFFRACTION100
3.76-3.910.2252380.17214880X-RAY DIFFRACTION100
3.91-4.090.21632170.1644923X-RAY DIFFRACTION100
4.09-4.310.18912610.15454876X-RAY DIFFRACTION99.98
4.31-4.580.162450.13414900X-RAY DIFFRACTION99.98
4.58-4.930.14952500.13144903X-RAY DIFFRACTION100
4.93-5.430.17822710.14394849X-RAY DIFFRACTION99.98
5.43-6.210.19122480.16284926X-RAY DIFFRACTION99.96
6.21-7.820.20882830.17544868X-RAY DIFFRACTION100
7.82-45.760.1882440.15874925X-RAY DIFFRACTION99.4
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)
13.057213599670.319285657087-0.04868635107522.432112203830.2105397261722.632728892890.0634730723483-0.170127630210.156125797341-0.0816360967358-0.1091271868440.7375653394440.19085869133-1.012500072740.0204441198930.333761060511-0.0255278411236-0.07784417906910.780739560819-0.131159014270.7144513110514.5842288089-3.402971436634.0745209105
23.264528306850.5035960141231.005274874694.284923901821.053372185611.422130373680.1200662445330.0907518318807-0.314490504236-0.203071449285-0.2152785157850.4824992409040.212007050685-0.4832054572230.08786505422420.366656803023-0.0890220054199-0.003077810040010.536085666191-0.08615625293020.39941379235317.2418340884-13.5600752757-3.40854515574
31.397765857870.2698439676240.4045407033562.68818444860.7332168561351.308659381580.1725145412670.21456967736-0.26760690319-0.182469251594-0.0687286713583-0.09734421197110.2867895815880.0380635235769-0.1071400598470.3362040984940.02487814837010.01496439310030.413000888809-0.02744130400480.27754974820440.0331600329-9.988861545892.08393236914
41.91118889997-0.524051299534-0.007244741629983.50736196451.411854685555.168205959780.122792184692-0.3633814472190.267993731514-0.0259226720658-0.08194752178770.0473301002138-0.33774387676-0.193545121906-0.05951296466140.2657903381830.0005530183356350.06063920818790.353524895662-0.04391526429080.5065250283132.889530412531.557692013623.4693727288
51.88414439831-0.6346331265380.4326711079952.574613332690.9034539627620.9180789995180.0444248716249-0.768609090167-0.1974184236571.06276790085-0.09620963130410.2499394571941.00637733393-0.4896361937610.006481963496571.41232243451-0.265035287104-0.1688933403680.8518505649620.3060849552110.64647816431958.8846967579-11.832988810763.1315825685
61.47183232910.4405623202880.7863002216292.959363290940.1999281235223.100791983970.41273442189-0.511757974767-0.3551251592580.839287894691-0.0909614569278-0.5080897114020.622278536247-0.0616576989269-0.2567348284770.638969270127-0.074660679339-0.1729682472240.5217531590060.07870145358190.48212790840869.3010273707-2.9651212131849.4565991938
71.553602524530.8037341060740.9988989187172.091268288211.161765354852.43258142480.1486175042050.0938681186734-0.1561534895850.0845201215842-0.0227457668413-0.1727518755820.1915756411650.0967733540937-0.09073587233380.2206627605270.02939137219840.02989107456430.3822685816010.005164251531220.32108118644262.84291470620.3277776438825.2953925843
81.323513412671.683718942140.4537294426214.998017245680.2880442660680.758225922225-0.0140116122975-0.228929705791-0.6155120037060.326873738753-0.1011013951570.0410129257591.0218942913-0.4026040522370.1887538142621.47570870659-0.201589121276-0.1698571243110.5923765479820.006030409974921.0241174010147.9945391018-44.228072194626.0909566709
93.432537370371.349015734750.4352813139395.35731600274-1.176774137692.63052831687-0.2159077334990.7903169174980.290078957032-0.9375145748820.107660134354-0.04961450500790.3652672668840.4187356377740.114605837580.7065510353190.0767742751115-0.01810356507820.766809918120.107190524850.4037136512715.607126062553.01893348729.51609732436
101.80526748547-0.544383917870.8361895246633.73254105055-0.7208852438632.654573194380.1730527041370.3652053700980.311497840173-0.572740524993-0.06875985055320.8144777555710.0568795238349-0.12494414295-0.09117015997010.3447078760590.0306175146209-0.08877762781880.4805182840740.06145183048670.6450868211731.9729834756355.519081998822.5895771036
110.3827237548020.297058201610.9567264118492.761740056511.404198064393.43197508084-0.1972624099880.1113098150050.317734570727-0.149168332178-0.11710017962-0.0444913845215-0.3216180224860.3239465887370.3277789343780.349674769493-0.05408205610050.01268902612840.4653155602540.1298969770240.71883595331111.021344389465.695084235835.9451839733
120.627337174468-0.1961613367480.1645134308842.014032223660.296358140970.789727385051-0.0763772858815-0.07051627585710.1855941970480.16888207296-0.08923405003550.208045824632-0.0841074529033-0.08421434147940.1684601586730.2338601609760.003498148694350.04406616735630.387925439043-0.04039874724510.4494077673187.0772914108947.578850071149.1262519703
135.0676748667-2.16449295953-0.6765852035474.125174414481.360587804473.5102718411-0.131239669499-0.00793078094467-0.2928883167480.0127361548831-0.007072998220380.06696786065970.2617489375590.2112490003110.1548506379760.32116264622-0.04023413562170.05601503314170.2998970324850.002429924085610.30400107530717.12465163257.1902757912430.9296896225
144.22333975844-1.76917387423-0.4695243724964.078067015670.9586973771411.719439794090.0461437560287-0.1108862824830.4259118185080.2666672352210.0295193556217-0.7561552291180.1174138397430.56148564793-0.10971143470.3755582062560.00104208931874-0.09325570106410.6179003558980.07579761045310.47413433972259.255485309929.079540548974.3636895477
151.76083151056-0.6487465755830.595109530192.21810978744-0.3842904578920.8114586183650.1351263900640.00425672868748-0.3860144534250.0979816649751-0.05799078813880.06089874300410.2926203844990.176970504907-0.1083131864330.4602568607430.03791148655340.06618806075480.4572877165190.05170656633630.32483898672236.150543634317.186029606569.7977708855
161.876825483271.23447984290.08156185099212.89835334332-0.09092371965810.7271556049970.0700465262446-0.1467690767140.1132782193010.270495401818-0.06560944512470.145709584599-0.0103623754998-0.053548752272-0.007752978179830.3119445932940.01532890697050.07169762418740.400286491109-0.02854624647150.30346415079127.808649045749.309938233768.552674698
172.938912892910.4586203801030.460368516542.89086959321-1.013359334183.526540368640.05484962036610.7003124423420.207227797104-0.916860159359-0.274329704914-0.2767734046460.009347459120620.2042971204690.1567266280790.9893473642020.1838850352620.0977958602890.7326016337260.06806923595750.40660543249514.2386918557-60.8078165353.1728673945
182.47421513839-0.930429643130.4757294313942.51988117824-0.335898320974.20543059090.2499883686780.5681161792690.260638299864-0.691149528418-0.2820374995450.296985876019-0.490630420072-0.391322481680.04390943242920.7093047303810.162177023772-0.1104528006570.5095271202320.01325226065760.457794042289-0.204536063243-54.922715901212.8228423039
191.29839396029-0.6655821998350.3633660245531.721232330940.2752550403831.949915489380.01058493121530.2863109699780.556065231912-0.57056291771-0.2726937888290.00171579572396-0.9832208192820.01989198703410.2587089438340.8944444206110.118319259272-0.1232949370560.4770853136980.05420542538590.650885880091.60682796811-37.648853462729.186796155
201.33111376247-0.734569303596-0.1370647468212.928177259520.5714508901631.57058331868-0.02061010623980.0195941059170.162728418284-0.0940505678597-0.08642385330590.237176353249-0.233805371279-0.1873090186150.1064771703030.3566724832960.0443282305751-0.04055271867690.390627333273-0.06338455859120.4273927308090.0740084556235-59.067774398541.2862784524
215.63883257982-1.905351924030.1892909465185.151909929850.5554902998772.10897135494-0.19428475616-0.159768728016-0.3022700504060.01922592132790.03516428604510.05462075324170.186064205370.2792596058980.1326055365130.4334595042370.01924189571310.08900906301620.389100099887-0.001874720778130.32311559823317.9873322637-95.163820886539.5943217513
221.314247141160.4769490048081.594064506272.48871718012-0.1434269708742.13801183292-0.2836140347490.2769117813121.039118844230.242313205572-0.154286571973-1.42479643474-0.359649617220.6748351186970.3077110907010.597879553298-0.152447029496-0.2904604728660.944665801595-0.01232237122821.6231406370754.0045876365-52.433047417572.5900984886
232.853572968780.3151129482251.579326657671.28486701718-0.5750705817621.93793946807-0.396508777939-0.4677271517630.5194388409340.7326901480610.207992014105-0.835318029415-0.516766452240.2123380729810.1347924296990.6926983368710.0683926329827-0.2830102957140.566456770989-0.2047390119160.84699090981835.6118519289-53.080461364380.0283217776
244.14514642777-0.2585382747131.314174111543.56925185113-1.187025459483.45747563804-0.221460098359-0.605397053485-0.1649857290260.719873559020.255106662508-0.769204470264-0.235402389330.208646525067-0.04984415817030.5869808826710.00362215933614-0.2731035595110.585794969906-0.128724401440.7382568885340.8077481643-62.317610025983.2302886719
252.664835441310.6778984538891.503899723362.43506917076-0.1980699848012.15172223920.4315045236680.113716276944-0.6613070911730.14176040237-0.00564979815628-0.3877026159670.538585681610.222416271953-0.4222717564520.5265307934520.0762150962107-0.2326802897920.450455404832-0.09543998039870.80750454318431.0217135023-75.130063472870.8779196999
262.37850298455-1.108862520271.11751338674.81018709514-1.250614736932.518902269460.135080853779-0.283864671515-0.529827721340.1734740680030.121465938154-0.1545911946090.294941953711-0.235364312012-0.2817781165250.388310205352-0.087201497648-0.0837375645010.439077504246-0.03998364764110.45060265504915.0940121825-70.675763391467.0000764099
272.122791133640.6653549004180.5207647844752.81786492099-0.2716117057751.795881462110.0728125231363-0.208542417387-0.04460670215430.151442098561-0.0804337900022-0.239752120252-0.185728386939-0.1681884114320.01641108174730.3800921684670.0336335542825-0.002643499264480.415359413673-0.1094064014560.38359637488912.9081684525-53.268378073664.5258391015
281.556223795880.326743410858-0.416263939241.99812585451-1.494867508532.959710879760.03148372812480.1069952535660.552241709709-0.391587321848-0.130751495532-0.31578366914-0.6916321131020.09938969448390.0518554855941.19168336586-0.04537362693730.005919722730890.456776537578-0.02193491115750.95900639375720.960162876-18.329969964153.1551716022
291.342185622310.3431484493160.8844641863862.34778245496-1.146699272683.405918252510.009839825977970.538923470980.356007092524-0.206566804663-0.354883142171-0.48676279583-1.055569538190.4417699258080.3308416621521.18829022231-0.1102963258990.08530109947740.6021827161950.08486421740271.0647472870527.5176146482-16.946057200947.9198227273
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 141 )AA18 - 1411 - 124
22chain 'A' and (resid 142 through 255 )AA142 - 255125 - 235
33chain 'A' and (resid 256 through 523 )AA256 - 523236 - 503
44chain 'A' and (resid 524 through 623 )AA524 - 623504 - 603
55chain 'B' and (resid 18 through 100 )BB18 - 1001 - 83
66chain 'B' and (resid 101 through 255 )BB101 - 25584 - 233
77chain 'B' and (resid 256 through 517 )BB256 - 517234 - 495
88chain 'B' and (resid 518 through 623 )BB518 - 623496 - 601
99chain 'C' and (resid 18 through 100 )CC18 - 1001 - 83
1010chain 'C' and (resid 101 through 219 )CC101 - 21984 - 202
1111chain 'C' and (resid 220 through 286 )CC220 - 286203 - 266
1212chain 'C' and (resid 287 through 523 )CC287 - 523267 - 503
1313chain 'C' and (resid 524 through 623 )CC524 - 623504 - 603
1414chain 'D' and (resid 18 through 141 )DD18 - 1411 - 124
1515chain 'D' and (resid 142 through 356 )DD142 - 356125 - 336
1616chain 'D' and (resid 357 through 623 )DD357 - 623337 - 603
1717chain 'E' and (resid 18 through 118 )EE18 - 1181 - 101
1818chain 'E' and (resid 119 through 237 )EE119 - 237102 - 213
1919chain 'E' and (resid 238 through 354 )EE238 - 354214 - 330
2020chain 'E' and (resid 355 through 523 )EE355 - 523331 - 499
2121chain 'E' and (resid 524 through 623 )EE524 - 623500 - 599
2222chain 'F' and (resid 18 through 99 )FF18 - 991 - 82
2323chain 'F' and (resid 100 through 174 )FF100 - 17483 - 157
2424chain 'F' and (resid 175 through 219 )FF175 - 219158 - 202
2525chain 'F' and (resid 220 through 303 )FF220 - 303203 - 279
2626chain 'F' and (resid 304 through 354 )FF304 - 354280 - 330
2727chain 'F' and (resid 355 through 523 )FF355 - 523331 - 499
2828chain 'F' and (resid 524 through 567 )FF524 - 567500 - 543
2929chain 'F' and (resid 568 through 623 )FF568 - 623544 - 599

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