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- PDB-8cjf: AetF, a single-component flavin-dependent tryptophan halogenase, ... -

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Basic information

Entry
Database: PDB / ID: 8cjf
TitleAetF, a single-component flavin-dependent tryptophan halogenase, in complex with 5-bromo-L-tryptophan
ComponentsAetF
KeywordsFLAVOPROTEIN / single-component flavin-dependent halogenase / Aetokthonotoxin / single-component monooxygenase / tryptophan halogenase
Function / homologyFAD/NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / 5-bromo-L-tryptophan / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / AetF
Function and homology information
Biological speciesAetokthonos hydrillicola Thurmond2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsGafe, S. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF.
Authors: Gafe, S. / Niemann, H.H.
History
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AetF
B: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,83012
Polymers154,1972
Non-polymers2,63310
Water11,367631
1
A: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4156
Polymers77,0991
Non-polymers1,3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AetF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4156
Polymers77,0991
Non-polymers1,3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.700, 122.700, 87.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 17 or resid 19...
d_2ens_1(chain "B" and (resid 1 through 17 or resid 19...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETVALVALAA1 - 179 - 25
d_12GLUGLUPHEPHEAA19 - 5527 - 63
d_13THRTHRASPASPAA57 - 19765 - 205
d_14LEULEUSERSERAA199 - 248207 - 256
d_15PROPROARGARGAA250 - 318258 - 326
d_16PHEPHETYRTYRAA320 - 346328 - 354
d_17TYRTYRTHRTHRAA348 - 369356 - 377
d_18PROPROALAALAAA371 - 495379 - 503
d_19VALVALSERSERAA497 - 655505 - 663
d_110FADFADFADFADAC701
d_11164X64X64X64XAD702
d_112PEGPEGPEGPEGAE703
d_113PEGPEGPEGPEGAF704
d_21METMETVALVALBB1 - 179 - 25
d_22GLUGLUPHEPHEBB19 - 5527 - 63
d_23THRTHRASPASPBB57 - 19765 - 205
d_24LEULEUSERSERBB199 - 248207 - 256
d_25PROPROARGARGBB250 - 318258 - 326
d_26PHEPHETYRTYRBB320 - 346328 - 354
d_27TYRTYRTHRTHRBB348 - 369356 - 377
d_28PROPROALAALABB371 - 495379 - 503
d_29VALVALLEULEUBB497 - 609505 - 617
d_210CYSCYSSERSERBB628 - 655636 - 663
d_211FADFADFADFADBH701
d_21264X64X64X64XBI702
d_213PEGPEGPEGPEGBJ703
d_214PEGPEGPEGPEGBK704

NCS oper: (Code: givenMatrix: (-0.0439606717348, 0.998703812021, 0.0256545355659), (0.99898403924, 0.0436890986214, 0.0110522398507), (0.0099170905358, 0.0261143354525, -0.99960977026)Vector: 64. ...NCS oper: (Code: given
Matrix: (-0.0439606717348, 0.998703812021, 0.0256545355659), (0.99898403924, 0.0436890986214, 0.0110522398507), (0.0099170905358, 0.0261143354525, -0.99960977026)
Vector: 64.4959800844, -58.446095281, -42.3887712734)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AetF


Mass: 77098.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria)
Gene: aetF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B9Z9

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Non-polymers , 5 types, 641 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-64X / 5-bromo-L-tryptophan


Mass: 283.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Condition A6, Morpheus Green Screen (Molecular Dimensions), 30 mM CaCl2, 30 mM MgCl2, 0.1 M HEPES/MOPS pH 7.5, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 6 mg/mL AetF (50 mM HEPES pH 7. ...Details: Condition A6, Morpheus Green Screen (Molecular Dimensions), 30 mM CaCl2, 30 mM MgCl2, 0.1 M HEPES/MOPS pH 7.5, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 6 mg/mL AetF (50 mM HEPES pH 7.0, 100 mM NaCl, 1 mM DTT), drop with 300 nL protein + 300 nL reservoir, 300 nL saturated 5-bromo-L-tryptophan dried up on plate prior to adding protein and reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 201422 / % possible obs: 99.8 % / Redundancy: 6.91 % / Biso Wilson estimate: 38.8 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.193 / Net I/σ(I): 6.55
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 7.07 % / Mean I/σ(I) obs: 0.43 / Num. unique obs: 32268 / CC1/2: 0.191 / Rrim(I) all: 2.616 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEMXCuBE3data collection
XDSBUILT=20220110data reduction
XDSBUILT=20220110data scaling
PHASER2.8.3phasing
Coot0.9.4.1 ELmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8CJD
Resolution: 1.9→46.48 Å / SU ML: 0.2808 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2075 9993 5 %
Rwork0.1831 189995 -
obs0.1843 199988 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.28 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10563 0 168 631 11362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311130
X-RAY DIFFRACTIONf_angle_d0.578515103
X-RAY DIFFRACTIONf_chiral_restr0.04321588
X-RAY DIFFRACTIONf_plane_restr0.00461944
X-RAY DIFFRACTIONf_dihedral_angle_d13.86744093
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.589949660448 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39962960.37745866X-RAY DIFFRACTION91.74
1.92-1.940.38473200.36356169X-RAY DIFFRACTION96.2
1.94-1.970.33463310.34856269X-RAY DIFFRACTION99.35
1.97-1.990.34453340.3326343X-RAY DIFFRACTION99.63
1.99-2.020.3123410.3226457X-RAY DIFFRACTION99.88
2.02-2.050.35193290.3146267X-RAY DIFFRACTION99.86
2.05-2.080.32933300.30166325X-RAY DIFFRACTION99.94
2.08-2.110.32773360.28846391X-RAY DIFFRACTION99.97
2.11-2.140.30163380.28276380X-RAY DIFFRACTION99.94
2.14-2.170.27783280.27656279X-RAY DIFFRACTION99.92
2.18-2.210.26653370.26376431X-RAY DIFFRACTION99.9
2.21-2.250.28773350.25286355X-RAY DIFFRACTION99.94
2.25-2.30.25713330.24066333X-RAY DIFFRACTION100
2.3-2.340.26213350.22936355X-RAY DIFFRACTION99.96
2.34-2.390.24133390.22276369X-RAY DIFFRACTION99.97
2.39-2.450.23853370.20996352X-RAY DIFFRACTION100
2.45-2.510.21413370.20076388X-RAY DIFFRACTION100
2.51-2.580.24863340.20466343X-RAY DIFFRACTION99.99
2.58-2.650.22653340.19596365X-RAY DIFFRACTION99.99
2.65-2.740.22353370.18966410X-RAY DIFFRACTION100
2.74-2.840.21113340.18286336X-RAY DIFFRACTION100
2.84-2.950.22913370.18356364X-RAY DIFFRACTION100
2.95-3.090.21693360.18696360X-RAY DIFFRACTION99.99
3.09-3.250.19033360.18066335X-RAY DIFFRACTION99.99
3.25-3.450.20823340.17036351X-RAY DIFFRACTION100
3.45-3.720.20973400.16126371X-RAY DIFFRACTION99.97
3.72-4.090.16783340.13386357X-RAY DIFFRACTION100
4.09-4.680.13453340.12016372X-RAY DIFFRACTION100
4.68-5.90.13423370.1356368X-RAY DIFFRACTION99.99
5.9-46.480.17363300.15346334X-RAY DIFFRACTION99.54
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)
14.656840928010.337842017331-1.501445018512.685197556570.715649355491.8410980074-0.0519089962387-0.0709327530438-0.1668830897720.289087508852-0.0157171422004-0.07800883203090.2650340875120.01706892138420.0624314494790.3603251363630.037206501669-0.04405000937350.3282777217930.007403888687990.24729237237348.4474932677-42.744890149113.8922101724
28.506932200814.907727086181.444368998944.804310618651.120618224053.34492750260.040411788319-0.544562912667-0.3890212143770.423476287242-0.2720493176010.03627954656250.423099572463-0.2378542804460.2117224976290.4457356495520.04977981660050.07328887607530.257880731353-0.04131501689980.29273444660141.4548012309-51.831252231214.0865072047
33.236417259110.648741486551-1.03467965362-0.00978965747004-0.1640474541590.4805111651180.07349164279360.0773945539381-0.3472705965350.133822061233-0.176446174965-0.03949162317490.108744993644-0.04012381871090.09569038756610.480141175897-0.02303563660040.04044460518030.392468748648-0.04029186494260.48940417035649.6710034583-53.83069135712.56629978753
42.9897435191-2.84503087657-1.733722405425.320023450682.430961560322.79017707921-0.0945823600313-0.1098207843170.3341206926440.2420044433550.10909512882-0.3158242820060.1018279236150.078927260427-0.05354186525470.313267706539-0.0450779746599-0.01091537739920.3480147656810.01811084502020.35029320719662.2871722765-37.0321539785-7.39739944471
51.21877004402-0.384358993739-0.2265224464770.9281874540690.1921741773720.388622071959-0.002056249174950.0500033687970.0672028083758-0.0402946258181-0.03246584236220.00800974343252-0.0419339851054-0.02326882053880.04102634614090.3511659033-0.00394237232212-0.0105222759790.374704350410.009170035498930.34709875632858.9511357438-33.0310289851-10.8601936135
60.1021607423190.192712797057-0.2813804164250.9348033158870.371705282820.8627370799130.0205241900532-0.130685471968-0.02740519239650.0136137777672-0.1669060840310.2350752352960.0833011490641-0.08510103855140.1601289730880.376609173863-0.0129390554182-0.002850094633290.352730884589-0.03028793382950.39445476105838.1032428032-46.6507780457-2.07891194008
71.434502190250.366976837866-0.03368753814321.479540774270.04574488573060.6658356317930.0748397281202-0.06619293108020.1731893702880.0789792315973-0.1475281390250.213107470279-0.0808339689731-0.07877991356220.06907169219680.2968640041340.01395950402670.0160439701690.337386917727-0.06049899716860.37544143112639.5465400283-26.63009561897.06848491492
85.72489511879-6.526030895182.068667481998.82023287869-2.857778500852.769491946650.0443856714269-0.01653306411380.431059493643-0.264980237834-0.0345098638401-0.390464886809-0.1267829512850.09826249340370.01391749465310.302711930662-0.0657032570551-0.006890582794160.347942216929-0.004121574255010.3227388045966.3775802507-25.789877416-7.83411641059
91.755017099880.494506250055-1.029433099740.8776374830781.285318990944.194400862080.2435726399660.1461866587550.0823199911129-0.763654789951-0.206230160455-0.323042917764-0.08406438467850.2185704533430.009431818521160.286124582929-0.06763885815510.06419457740290.4801729409790.09607032699980.42280045542273.5226020341-32.8662809105-18.8658012767
104.997627279340.996450537364-1.017141624452.77109219170.08200228235321.002556217710.2258307553910.05085095094041.002926624510.14365582999-0.0635243694240.211735397532-0.38956340089-0.0628635370691-0.2041338232760.5057919689240.0373201858614-0.01720268141320.359051496688-0.01815583818820.51685088540344.284890741-8.590825933252.11883588787
111.73829907974-0.111761655741-0.6007294176613.634454043691.208454649241.827936216170.05468904819250.235616433513-0.00178059549237-0.0735492002763-0.09142730375550.195002568691-0.0732817526062-0.4473987390230.03530103171650.3439255996080.0403913729366-0.02753181074170.4273165285780.01329472382630.20375316398719.8347494129-11.7222418087-56.999760385
123.461183140893.38422928547-1.125208910777.85195395637-2.064959901482.50988603639-0.1397999313650.467875009242-0.139562274294-0.5254895222160.06112184350070.2956487486680.194863785095-0.4745748677190.06791228282040.3175681293940.0222610750292-0.02943659811330.55650184026-0.08443383226610.3272481708911.2069272219-19.0342217788-57.3259393466
130.06403346297410.3170374404350.2509075093674.142276793051.329359310481.0741291286-0.04321397054530.113455227969-0.0205683485912-0.06468463112620.09112083409090.206416018994-0.00878864091536-0.144669403302-0.01835197352210.337339715287-0.02941210401520.02010180034390.535790273098-0.01830777129050.4502648861828.6437579465-11.1132808388-45.8205762696
146.61285318276-3.82894208212-2.22243471763.002291022121.886672765082.311607999620.3003074254310.3215809270140.277579050672-0.104620259642-0.168767721465-0.299972067041-0.139206246921-0.0863174996106-0.1683751973580.326488583397-0.0375237848911-0.03768749209840.283562910185-0.0051517684730.27330816586524.87997458341.8313802733-35.7685913917
150.533581032011-0.365605411622-0.6178684042391.067449826450.6811916943250.9438587472260.05089152520630.03233141214910.03223676010970.0543406305168-0.0171036983764-0.0589040991394-0.00447869295564-0.00846037263235-0.02750404679610.363822073217-0.0143068632981-0.03638266235120.3346903643530.003057991916850.30058349082226.7229971651-2.03657409972-32.1917529283
162.08819573735-0.102309193209-0.4055280685691.205739535940.2747496275051.37985354971-0.0601262501538-0.00884164352983-0.2571619702770.0167871868996-0.0186845304407-0.07816501110740.17898508937-0.1161811942970.0842411111180.319410986934-0.003799234941770.01628745839910.287496946909-0.03257977117990.29693909271929.589784269-24.4812551698-47.6388568754
170.664213595098-0.182767032757-0.6954862550881.040297577710.9046068172823.671481467410.0333591570832-0.06170885986780.1593020056230.02834993432890.104046599272-0.3170388177110.06835949712880.398463075443-0.1659348407420.300775313214-0.0297293672687-0.003284449164890.377786665335-0.04535440105190.48011772863844.8231161594-3.38551393647-41.2081667801
180.6693739578250.31629645157-1.064136525611.885323028140.4434879645695.898456820880.2065443512120.01638168246790.168415203953-0.212096847533-0.08230668728150.0276692488066-0.692963682553-0.425998489956-0.09555087115180.4956196783970.03983642367490.01187111781450.296645679852-0.02266034215640.38008884097419.656080618317.0514068638-31.8310166006
194.29721389661-3.36025621676-4.409832543214.872363765225.655191428696.685352908070.391234012835-0.5397340011260.745237874663-0.2562649702760.603198235899-1.01867291041-0.5474553076320.905131163479-1.127029274850.412372215442-0.068509312743-0.02894003828590.484317548667-0.08856341843240.55499428619447.87233079524.21804269979-32.071303646
205.913087361471.736057814320.1326127486634.769718717480.2616213018961.85072056133-0.1734693889790.206205844172-0.5250238371280.05643088803750.452800650122-1.482245703020.04682431834840.395972044623-0.2454500080570.4132000875110.06955090744650.02216612139870.453277987853-0.1313589326430.67399898467653.8462882759-20.1408751198-44.7003230292
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 75 )AA1 - 751 - 75
22chain 'A' and (resid 76 through 113 )AA76 - 11376 - 113
33chain 'A' and (resid 114 through 148 )AA114 - 148114 - 148
44chain 'A' and (resid 149 through 199 )AA149 - 199149 - 199
55chain 'A' and (resid 200 through 319 )AA200 - 319200 - 319
66chain 'A' and (resid 320 through 375 )AA320 - 375320 - 375
77chain 'A' and (resid 376 through 504 )AA376 - 504376 - 504
88chain 'A' and (resid 505 through 548 )AA505 - 548505 - 548
99chain 'A' and (resid 549 through 585 )AA549 - 585549 - 585
1010chain 'A' and (resid 586 through 655 )AA586 - 655586 - 637
1111chain 'B' and (resid 1 through 75 )BF1 - 751 - 75
1212chain 'B' and (resid 76 through 113 )BF76 - 11376 - 113
1313chain 'B' and (resid 114 through 148 )BF114 - 148114 - 148
1414chain 'B' and (resid 149 through 199 )BF149 - 199149 - 199
1515chain 'B' and (resid 200 through 334 )BF200 - 334200 - 334
1616chain 'B' and (resid 335 through 479 )BF335 - 479335 - 479
1717chain 'B' and (resid 480 through 530 )BF480 - 530480 - 530
1818chain 'B' and (resid 531 through 568 )BF531 - 568531 - 568
1919chain 'B' and (resid 569 through 601 )BF569 - 601569 - 601
2020chain 'B' and (resid 602 through 655 )BF602 - 655602 - 638

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