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- PDB-7mci: MoFe protein from Azotobacter vinelandii with a sulfur-replenishe... -

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Basic information

Entry
Database: PDB / ID: 7mci
TitleMoFe protein from Azotobacter vinelandii with a sulfur-replenished cofactor
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Azotobacter vinelandii / MoFe-protein / nitrogenase
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER / HYDROSULFURIC ACID / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / MOLYBDENUM ATOM / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase molybdenum-iron protein alpha chain
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKang, W. / Lee, C. / Hu, Y. / Ribbe, M.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM67626 United States
Department of Energy (DOE, United States)DE-SC0016510 United States
CitationJournal: Nat Catal / Year: 2022
Title: Evidence of substrate binding and product release via belt-sulfur mobilization of the nitrogenase cofactor
Authors: Lee, C.C. / Kang, W. / Jasniewski, A.J. / Stiebritz, M.T. / Tanifuji, K. / Ribbe, M.W. / Hu, Y.
History
DepositionApr 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase molybdenum-iron protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
C: Nitrogenase molybdenum-iron protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,86431
Polymers229,7984
Non-polymers5,06727
Water25,0411390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35950 Å2
ΔGint-308 kcal/mol
Surface area55700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.834, 73.995, 208.766
Angle α, β, γ (deg.)90.000, 103.051, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD

#1: Protein Nitrogenase molybdenum-iron protein alpha chain / Dinitrogenase / Nitrogenase component I


Mass: 55363.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase


Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DGZ8, nitrogenase

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Non-polymers , 8 types, 1417 molecules

#3: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#6: Chemical
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mo
#7: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1390 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M CHC (pH5), 0.16M ammonium acetate, 25.6% (v/v) glycerol, 2% MPD, 0.1M CsCl, 1mM Dithiothreitol, 5mM Eu-EGTA, 16% PEG smear high

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.65→38.94 Å / Num. obs: 292285 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.089 / Net I/σ(I): 3.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 14452 / CC1/2: 0.628 / Rpim(I) all: 0.841 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7Q
Resolution: 1.65→38.22 Å / SU ML: 0.2002 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1952 14399 4.93 %
Rwork0.1721 277585 -
obs0.1732 291984 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.14 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15764 0 170 1390 17324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009516352
X-RAY DIFFRACTIONf_angle_d1.11522236
X-RAY DIFFRACTIONf_chiral_restr0.06482334
X-RAY DIFFRACTIONf_plane_restr0.00752846
X-RAY DIFFRACTIONf_dihedral_angle_d9.51532202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.35814680.35239174X-RAY DIFFRACTION98.24
1.67-1.690.34615110.33549315X-RAY DIFFRACTION98.63
1.69-1.710.33574800.31579145X-RAY DIFFRACTION98.45
1.71-1.730.31294900.30269244X-RAY DIFFRACTION98.51
1.73-1.750.31444850.28879268X-RAY DIFFRACTION98.34
1.75-1.780.28854630.27179203X-RAY DIFFRACTION98.43
1.78-1.80.34540.26129266X-RAY DIFFRACTION98.1
1.8-1.830.29564580.25389231X-RAY DIFFRACTION98.06
1.83-1.860.2834140.25069305X-RAY DIFFRACTION98.21
1.86-1.890.26344830.23559116X-RAY DIFFRACTION97.78
1.89-1.920.25124700.22179094X-RAY DIFFRACTION97.24
1.92-1.960.23584740.20879085X-RAY DIFFRACTION96.11
1.96-1.990.23514760.20259000X-RAY DIFFRACTION95.92
1.99-2.030.22514940.18789286X-RAY DIFFRACTION98.76
2.03-2.080.20774710.18419286X-RAY DIFFRACTION98.78
2.08-2.130.19725010.17919262X-RAY DIFFRACTION98.6
2.13-2.180.20624740.17519304X-RAY DIFFRACTION98.87
2.18-2.240.18714510.17089354X-RAY DIFFRACTION98.9
2.24-2.310.1885130.16029260X-RAY DIFFRACTION98.72
2.31-2.380.17794990.16299276X-RAY DIFFRACTION98.74
2.38-2.460.20074820.16239230X-RAY DIFFRACTION97.65
2.46-2.560.19424380.16488924X-RAY DIFFRACTION94.81
2.56-2.680.18914710.16159386X-RAY DIFFRACTION99.32
2.68-2.820.19834990.16129390X-RAY DIFFRACTION99.49
2.82-30.17375050.15559355X-RAY DIFFRACTION99.39
3-3.230.18535170.15189369X-RAY DIFFRACTION99.06
3.23-3.550.17315020.14789325X-RAY DIFFRACTION98.42
3.55-4.070.15484800.13459135X-RAY DIFFRACTION96.27
4.07-5.120.13944990.12329476X-RAY DIFFRACTION99.11
5.12-38.220.16254770.15139521X-RAY DIFFRACTION97.49
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)
10.872416435434-0.06283517611930.2920111853020.4767732090240.1316756816881.06408087948-0.003870722148780.251863741778-0.0637693019101-0.1332997420240.04395644537550.09783267663160.0826882903179-0.0730909877968-0.04773909956650.349267109712-0.057615759247-0.008221928123790.3237588064810.01245591104730.18156447457833.176889437525.12509460279.16910682584
20.783438757845-0.2440698872790.3232393191691.32699711634-0.3037275672632.02843209983-0.02976972442940.1197622035210.153094909248-0.09119836537280.0537000024577-0.127664529971-0.2331303614490.234282381745-0.008417245087460.257770486076-0.06463963165080.02666367114410.244907909404-0.007768608107640.1759892673154.463974866439.443515304323.3484136683
30.4524620522910.000299532790658-0.03656134756450.3916470310840.04920625927070.797896467344-0.002077397400380.126511457665-0.0743873745232-0.0587537680890.0550184260167-0.02983080072880.1917067764320.0575027940516-0.05181871798810.350739301349-0.0272079769852-0.007892900383850.271377559488-0.03565645812020.18840342923845.709627745813.629882788315.5408625008
42.23592197186-1.00410369343-2.790755300361.247888846030.9840377127243.57489146084-0.1154086205290.295834406957-0.1332627007890.05999227213910.0816226359040.1027170157750.252393282724-0.3320924898480.04342756087330.329736000989-0.0986827948748-0.02980153661340.221772402139-0.002129873236250.16760056228830.3205690810.655966442329.5955761895
50.780597235806-0.1058688999420.08538081722520.9402321814550.4441493859360.911078444850.04958798572690.0582239211515-0.02164086481410.0816604469380.0444684894598-0.1024775380050.1018713526970.256573461444-0.09556561662440.237911789689-0.014488286029-0.001648037710770.273836201107-0.01127510194070.12164972270356.937416607325.110861694935.5298555949
60.305316704937-0.08286262622280.1813076961090.872944083535-0.6462918758722.271406030240.01790112373060.119969154040.0708443186694-0.119608619190.0322593255230.0605853708738-0.15866019701-0.185366360747-0.04818009981020.289652050159-0.002095981788820.006128051001120.2735646033210.04104754871820.17763776187126.573820602741.479127820815.4415952358
71.10860980192-0.0435890759731-0.2521641028090.239076169280.3520634732951.007531141920.01736633400710.06756239825540.153598740422-0.1322203011730.00687328312470.0476509917235-0.249325047552-0.283244642971-0.02885931511770.3021571359110.05288608776660.002525240027970.2807848414570.05142364731080.1883442722417.096271323546.709514935533.4918096758
80.709090612565-0.4259295255630.3501518023561.718467497270.4363800102321.80070709361-0.02847558951440.04558770549340.157025440104-0.14402720338-0.01877961300930.0675521620255-0.449296284332-0.2950145393670.06247892596090.2745774743180.05521874375830.03667813781590.2870495992920.06665792687420.18607943048318.423463669449.735570440932.7586416359
90.931956966268-0.145602882792-0.2480926757490.2743969443690.02632202779671.559037474440.06018454804080.03046954628340.14316574136-0.02420970255050.006687868998670.0142669139745-0.24312358454-0.132026399622-0.06751252242870.2725683827890.01124527292770.0257127823230.1629108713740.006743918527930.18728829729128.840818074245.548631470252.5301462206
100.7191495409980.03719709456960.1206830371520.3872737008960.1890416546420.9370558015410.02340521260420.02962452996070.0730403474349-0.006650937697260.0179620257149-0.00800923578107-0.1071706760290.0685525670178-0.0451000471760.25273807357-0.03223411459360.01478276365830.1852867380740.01376418512340.16120084623843.078188727438.855188070445.1443543754
114.92413365882-3.835266418823.05343974743.67891742421-2.977611538942.716224284990.1429249482790.241030902493-0.0401441012453-0.065622506821-0.14594956390.02079790802130.1272084478440.08735877475450.002192509965370.217314299778-0.0341694093790.006104194790960.129224110019-0.02224598044560.10827584987937.951880574227.718768800159.8455160242
122.127423960360.04194194177010.8159947862411.628043860660.4318495868211.5548910879-0.0486237920062-0.2934992002930.2182592361050.200505294907-0.01132595926490.074578524827-0.177525941912-0.3149369912090.05597223452110.3276811388910.01548298853390.04849962555650.369408379256-0.03336764370640.20805475685720.877873442741.422913887397.5082176241
130.991275735472-0.132065304793-0.02847354274580.375067256842-0.0646684619570.789683420717-0.0145473021653-0.108176742991-0.1446212088860.05142264134830.05123227479430.04325365210160.258769656897-0.137886750068-0.02414962183860.273690139353-0.05196692810480.004212441020770.1718352931250.03001149515910.15219353215632.706938614610.962020642480.3896297247
140.7103909992020.06263276684230.264082590030.3001080407480.158274583720.6675061118810.0390449222206-0.0874604785364-0.1141587035750.08434366592460.00989834299945-0.001684578029180.172665514816-0.0137568743983-0.04991759639680.321026140488-0.01455013204340.0004401848326630.2281463611440.03015075550710.19315675847844.940653882313.833325448589.4361451136
150.652799169672-0.007141635295660.1431587231160.544721922563-0.2161912902440.9177063083570.0117868156449-0.1020946588650.04853536448950.0938881363957-0.0161878646104-0.0211881676684-0.1040587601820.04235560097920.007445417842340.246831950171-0.0264812760760.007661822856390.188258596886-0.01552789390760.15236272914846.846049917436.438096158489.0830270294
160.717550229296-0.1189294054320.9609879090430.926751209402-0.4147165177485.7393862079-0.0467990499047-0.1606874422090.09528690092340.06638924692460.03969730926710.0616524854906-0.170106632385-0.3879458978710.009561980030290.1878488315360.01013997566070.03892924657920.192983127537-0.009112172284960.17254586112727.200438339739.933198368585.20299166
173.33085723569-0.6102119764573.784962528610.972015850961-1.533293001255.19244440629-0.113099289001-0.02692696463560.1314061185890.1263117520370.0804770193487-0.00486753861991-0.267561389169-0.1900955471110.04517209985590.2275900131540.005253580918190.04506306886590.151250634854-0.005343005369950.14044633369536.216586937541.240363769571.8786893199
181.141913643860.04074432949620.3454766642750.6878092734440.3246268634221.062157162490.01811237207690.0353997393022-0.164688664421-0.02593965456730.0741876956792-0.0886850222740.2138043890930.101903418389-0.096431554770.253343994190.0100821703720.007946070665010.1597555314950.007452751683440.12579820052448.348145177813.09451527170.8309397729
191.09619066170.429069506667-0.9154871988221.48115365121-0.9388611041642.562194263810.0458119313103-0.147589258883-0.01615565470070.1678470097990.06611500033510.172115443353-0.0287822036955-0.332444669718-0.1084632391710.186179221292-0.04434226192110.02068453764310.2636579338280.02537118109370.15605754119316.540142100622.125017074979.0015302191
200.261056644743-0.0931744400348-0.003488542712120.2255645035630.07304204488990.7521019119490.00875220533742-0.0861204821999-0.05777366127070.06487638736270.0178615057290.1491495045530.124317855341-0.510096576756-0.02196856333910.2451118882-0.0930074433270.03628763902650.4532004289610.04732314102370.2523596913594.8592401499519.613165678575.0954178724
213.120057534282.394604257221.443531418441.980893162661.005939821751.27833536436-0.0167808608425-0.06287283331260.0729871037563-0.03383667461890.01128836099420.174315051547-0.0522637796126-0.4318433166120.007479024963330.197399938882-0.006348542490640.01752788461580.3462828255970.03889916555770.2170221364399.4052850261631.741010030664.6562830065
220.823243814551-0.0294620026924-0.6262590057330.332187788874-0.02094888584261.44862439702-0.02393371024090.0448762783508-0.07292288197350.004436660640820.04610338713490.1568061836910.217256578369-0.530155510463-0.007187491199130.240608954425-0.132348053488-0.01883964051820.3990094636640.03838401781850.225013498596.5699447584115.695762114151.4932953179
230.443335763554-0.02059563377940.2789030308830.664648850524-0.07433832875331.010676938740.02217508975710.0185223913605-0.132469543164-0.01448818384290.03997570202680.0710740749220.297922877896-0.126610501607-0.06163578708890.29558112748-0.0722659657797-0.0002486886104510.1844675121290.01017188659410.18018743898529.29723193399.5192920082555.9002363696
246.66425407822-0.239352021754-3.165221821020.2712280975130.03942176588572.1700826401-0.10133030748-0.07806887193650.0142283076021-0.02259917767210.101195462243-0.01067972865150.1316123386410.02740887295350.000713485480310.279427893127-0.0415012413454-0.01397336039370.144151584676-0.01042065266530.14258526176137.600605400920.81220008142.5592527333
250.222990035504-0.487052770799-0.1111419090933.295380269171.34335099350.6325166227940.0408436318830.1609210219860.01603707122480.0981172844961-0.0627446424126-0.1078409823840.010232573883-0.0323896958980.02820435594860.287860134861-0.03976129865440.01243231420420.2553891335520.00248630614620.17874200907840.653246809828.747747739718.0933983134
261.916423440021.945888712450.6559087651882.285718697710.6117463125410.232365104378-0.0322631051134-0.130308396769-0.1172917176990.005148205452630.02066668711930.01312453922830.13420251227-0.2093925200760.02069510466530.244216278198-0.03934870973050.01962320056230.2499659837860.01574751029650.197344375330.142766207821.657604035783.9120761623
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 91 )AA4 - 911 - 88
22chain 'A' and (resid 92 through 174 )AA92 - 17489 - 171
33chain 'A' and (resid 175 through 440 )AA175 - 440172 - 439
44chain 'A' and (resid 441 through 480 )AA441 - 480440 - 479
55chain 'B' and (resid 2 through 70 )BJ2 - 701 - 69
66chain 'B' and (resid 71 through 192 )BJ71 - 19270 - 191
77chain 'B' and (resid 193 through 264 )BJ193 - 264192 - 263
88chain 'B' and (resid 265 through 320 )BJ265 - 320264 - 319
99chain 'B' and (resid 321 through 399 )BJ321 - 399320 - 398
1010chain 'B' and (resid 400 through 485 )BJ400 - 485399 - 484
1111chain 'B' and (resid 486 through 523 )BJ486 - 523485 - 524
1212chain 'C' and (resid 4 through 49 )CR4 - 491 - 46
1313chain 'C' and (resid 50 through 141 )CR50 - 14147 - 138
1414chain 'C' and (resid 142 through 275 )CR142 - 275139 - 272
1515chain 'C' and (resid 276 through 383 )CR276 - 383273 - 380
1616chain 'C' and (resid 384 through 440 )CR384 - 440381 - 437
1717chain 'C' and (resid 441 through 480 )CR441 - 480438 - 477
1818chain 'D' and (resid 2 through 70 )DAA2 - 701 - 69
1919chain 'D' and (resid 71 through 127 )DAA71 - 12770 - 126
2020chain 'D' and (resid 128 through 246 )DAA128 - 246127 - 245
2121chain 'D' and (resid 247 through 277 )DAA247 - 277246 - 276
2222chain 'D' and (resid 278 through 362 )DAA278 - 362277 - 361
2323chain 'D' and (resid 363 through 485 )DAA363 - 485362 - 484
2424chain 'D' and (resid 486 through 523 )DAA486 - 523485 - 522
2525chain 'A' and (resid 501 through 503)AB - D501 - 503
2626chain 'C' and (resid 501 through 503)CS - U501 - 503

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