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- PDB-9g2a: Staphylococcus aureus MazF in complex with nanobody 4 -

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Basic information

Entry
Database: PDB / ID: 9g2a
TitleStaphylococcus aureus MazF in complex with nanobody 4
Components
  • Endoribonuclease MazF
  • Nanobody 4
KeywordsTOXIN / Toxin-antotoxin system / Ribonuclease / nanobody
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04659385326 Å
AuthorsProlic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Vrije Universiteit BrusselSRP13 Belgium
CitationJournal: To Be Published
Title: Staphylococcus aureus MazF in complex with nanobody 4.
Authors: Prolic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / De Bruyn, P. / Loris, R.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: Nanobody 4
D: Nanobody 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8858
Polymers58,9904
Non-polymers8954
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-0 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.970, 51.650, 70.340
Angle α, β, γ (deg.)81.260, 81.610, 71.650
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNILEILE(chain 'C' and (resid 5 through 54 or resid 59 through 68 or resid 70 through 128))CC5 - 534 - 52
121SERSERLYSLYS(chain 'C' and (resid 5 through 54 or resid 59 through 68 or resid 70 through 128))CC59 - 6758 - 66
131PHEPHEVALVAL(chain 'C' and (resid 5 through 54 or resid 59 through 68 or resid 70 through 128))CC70 - 12769 - 126
211GLNGLNILEILE(chain 'D' and (resid 5 through 54 or resid 59...DD5 - 534 - 52
221SERSERLYSLYS(chain 'D' and (resid 5 through 54 or resid 59...DD59 - 6758 - 66
231PHEPHEVALVAL(chain 'D' and (resid 5 through 54 or resid 59...DD70 - 12769 - 126
142PROPROLEULEU(chain 'A' and (resid 1 through 10 or resid 12...AA1 - 914 - 22
152LEULEUVALVAL(chain 'A' and (resid 1 through 10 or resid 12...AA12 - 5925 - 72
162ILEILEILEILE(chain 'A' and (resid 1 through 10 or resid 12...AA6174
172LYSLYSLYSLYS(chain 'A' and (resid 1 through 10 or resid 12...AA63 - 6476 - 77
182TYRTYRMETMET(chain 'A' and (resid 1 through 10 or resid 12...AA66 - 9979 - 112
192VALVALASPASP(chain 'A' and (resid 1 through 10 or resid 12...AA102 - 103115 - 116
1102ALAALAASNASN(chain 'A' and (resid 1 through 10 or resid 12...AA105 - 113118 - 126
242PROPROLEULEU(chain 'B' and (resid 1 through 10 or resid 12...BB1 - 914 - 22
252LEULEUVALVAL(chain 'B' and (resid 1 through 10 or resid 12...BB12 - 5925 - 72
262ILEILEILEILE(chain 'B' and (resid 1 through 10 or resid 12...BB6174
2112LYSLYSMETMET(chain 'B' and (resid 1 through 10 or resid 12...BB64 - 9977 - 112
2122VALVALASPASP(chain 'B' and (resid 1 through 10 or resid 12...BB102 - 103115 - 116
2132ALAALAASNASN(chain 'B' and (resid 1 through 10 or resid 12...BB105 - 113118 - 126

NCS ensembles :
ID
1
2

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Components

#1: Protein Endoribonuclease MazF / SaMazF / Toxin MazF / mRNA interferase MazF


Mass: 14952.206 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: mazF, SA1873 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7A4G9, Hydrolases; Acting on ester bonds
#2: Antibody Nanobody 4


Mass: 14542.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% w/v PEG20000, 20% w/v PEG-MME 550, 0.1 M MOPS/HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.04659385326→37.8590716537 Å / Num. obs: 29592 / % possible obs: 94 % / Redundancy: 1.96 % / Biso Wilson estimate: 22.6890905514 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.75
Reflection shellResolution: 2.04659385326→2.17 Å / Num. unique obs: 4611 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04659385326→37.8590716537 Å / SU ML: 0.375124675065 / Cross valid method: FREE R-VALUE / σ(F): 1.97682144033 / Phase error: 36.4972878768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.306648133329 1366 4.99963399458 %
Rwork0.239536835888 25956 -
obs0.242874958843 27322 86.8357487923 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.145290239 Å2
Refinement stepCycle: LAST / Resolution: 2.04659385326→37.8590716537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 56 145 3604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008409410891173556
X-RAY DIFFRACTIONf_angle_d1.097977053894840
X-RAY DIFFRACTIONf_chiral_restr0.0644529991148561
X-RAY DIFFRACTIONf_plane_restr0.00679461437991610
X-RAY DIFFRACTIONf_dihedral_angle_d14.43673124312145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0466-2.11970.342256970032940.3466577246371809X-RAY DIFFRACTION59.9558916194
2.1197-2.20460.4399674763811060.3189079130262087X-RAY DIFFRACTION70.3561116458
2.2046-2.30490.3845540288051310.3153392873722361X-RAY DIFFRACTION79.8206278027
2.3049-2.42640.3360244388881440.2835383989612772X-RAY DIFFRACTION91.4967053655
2.4264-2.57840.3608682450351510.272604517082867X-RAY DIFFRACTION95.90085796
2.5784-2.77740.3083294709211480.2709909181252814X-RAY DIFFRACTION95.0272698107
2.7774-3.05680.3362316736851510.2621584098992858X-RAY DIFFRACTION95.3724247227
3.0568-3.49890.3010619545921470.2368391877992798X-RAY DIFFRACTION93.3143219265
3.4989-4.40720.2484385043971460.1787371383312774X-RAY DIFFRACTION92.9640241961
4.4072-37.85907165370.2658121016451480.1945134011382816X-RAY DIFFRACTION94.2748091603
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)
14.50848243635-1.694859642752.542121468221.63393463567-1.716062265274.255546511380.2202052569360.462505768317-0.076868458432-0.227594569753-0.1565457205490.08662834959130.2485160653440.187690989435-0.03044945227110.0615737601150.0767403506750.03933966765710.156786970293-0.03221149352510.141780887895-29.0487868065-1.36206336796-30.7705232006
20.4726686050780.0203098523733-0.554015314509-0.00120463791297-0.006208253443171.07032921768-0.0510207910161-0.0286159722270.06029113411360.1392763357750.05962071292410.243420660459-0.0744362342968-0.194847878446-0.07415246151110.09353819445230.1446932342670.08817183228430.36783398399-0.09256650222940.374254819504-38.00957329756.24378216387-16.6517938572
31.133572590660.07543030411660.2590617217310.4069570691750.1616044303950.4054720680570.02312919359880.008597040031120.0251050349626-0.01858992652150.0199509533383-0.0104289829591-0.0113254755088-0.08619762189750.0828275705067-0.1214667616390.1359994058290.06175119782970.01154592245420.001122019312470.14845233834-33.0723763151-1.37379467995-24.0092840783
40.213883776867-0.325836230937-0.1737113257250.7582856354370.4198353616770.371489272235-0.05315597152980.1032332425460.226396945010.0666801526073-0.00788759317978-0.0864636755178-0.3017042563840.1781665368270.009999753210910.160549775909-0.0640154246998-0.01981928759710.170250784595-0.008317880367020.23699098992-22.53557287310.3417792253-14.8180511218
50.285279920731-0.04394355997420.213176969180.226594570644-0.01444304117520.1635362530640.0005831281984340.07443634016790.0812039283430.04229467281830.06319935163940.0123139614483-0.0449303738578-0.0869731303514-0.0323704976285-0.06751146258170.1336072955560.008550328341820.242467817184-0.03950095696540.287195819497-34.61153525581.86074209113-17.973549038
62.360570111240.6883321360870.441646484620.442630923992-0.09334936181950.8534921501290.01580062531570.1994468065280.174104280738-0.04870546364420.0194926859038-0.0355315757708-0.05610905542380.0498697572760.0193135146490.02526044080530.0242501325491-0.0050137744390.3485932525560.1222380133710.379550626844-28.78205866737.36696723214-28.0408807667
70.026864990294-0.08866107229610.05383311408870.398605176201-0.07605791328910.238807444470.01677591555230.1267601885760.08527074053780.03183101264140.0242172111647-0.1140356320370.01831977881340.09945239181780.05844494632140.04290488070850.107780158204-0.07655327741950.277385263371-0.02641581693870.304480203468-21.4230603389-4.68984835105-15.9814182948
82.57539664755-0.868527236229-1.731117612450.9837190566250.6801699760711.17649935501-0.00552610597451-0.282043188956-0.007967485299250.3669168620810.04088249038560.001421108623320.02246770161450.122226533125-0.0009996697846020.463224616595-0.04522491370320.02436307029130.2002931625380.0990445196810.16138288133-33.6388331764-12.1639675516-0.853144855362
90.000135923076756-0.0006125661359520.0004443055237660.0041908585108-0.0001816257438930.000746311838719.75683863588E-5-0.0666471292184-0.01056772487820.0859146056810.08453750576640.1135687529940.0585171692295-0.101336304158-0.06690662193580.501405616106-0.1553792993230.1825021682720.4898424842780.03651740044830.36673991901-44.2469336158-10.106900812-5.12982675334
100.41992224547-0.25485446785-0.2137828578920.1955554478680.1092363586610.119297702372-0.00779716452699-0.0410867271029-0.08203166311720.0209667345364-0.02069766927820.07881864222830.0186678230966-0.0409010805340.00640137363739-0.02279446737820.0413641494218-0.01442763559850.537926366260.07324478214630.362900953073-47.0832693379-3.17431709722-17.9361015369
110.821275208837-0.357187857929-0.5503562293131.854031143880.106984426611.009231071330.00709903690776-0.0909093394014-0.02065535978920.151126493220.0871687757730.06104067705030.24763724965-0.30974552824-0.058103089650.235650792645-0.02555031908560.03274454492310.2065528403840.005890816687510.136937374849-36.1649700903-7.90040558468-6.24283513034
120.105518117289-0.07156399940950.08898269258051.01297402420.2467281545250.1731946761640.17820019957-0.141236209151-0.08239061786110.259624345015-0.1526149144810.1958131977160.262569193877-0.218417821159-0.002581110577470.558566453232-0.237683393755-0.07634788013380.254932474305-0.03270017027450.221117971221-42.0480767912-19.5651389405-22.4691362892
130.009308482246720.0171735318516-0.02929792859540.0303662471455-0.05281853595550.09014695075770.0428524437736-0.0988922050172-0.09145804230140.105633763820.05965286736730.2805125393410.105070823911-0.273961762549-0.1409922445550.582183667212-0.262878493344-0.01881892813880.3522015405070.1455532347910.317713811318-44.0611490557-22.8800985719-12.0157816022
140.189507460397-0.2089273966370.05405002156730.7422485648190.8944166311861.791217596360.0677139829073-0.09007720139440.03166176608890.0612139868631-0.003560964904780.216067602520.130195375705-0.2420377735980.03847598432030.184102385705-0.01054283202810.05401675761580.294326157510.0115940829510.167954424563-40.3284991617-7.73110483027-12.203427674
150.741039882545-1.09578541124-0.5210935961483.290726757380.7914749846570.564551939969-0.0077216204779-0.139881950496-0.06946756803020.2342972124680.08225209231550.2236037547670.0161188598491-0.103142760654-0.01096438817560.651007199219-0.204302144740.01879086138140.5374137733640.1390892430410.254748204233-42.1431358273-15.5544182785-2.18417188866
160.5112356849630.2299902064410.1017698142341.43703980015-0.9447927358040.7555949489590.0169949916815-0.0294245457234-0.1769887805160.1020822334090.0241888902278-0.1815125195940.3658376534360.08149537386250.07181523668950.4056938477030.121644016232-0.05202571318320.106038917356-0.03976233751720.14489192477-29.4714799531-17.3108226594-15.6823489004
170.1303733910880.135266952338-0.171348715710.158247545206-0.1940478201720.24459126453-0.05103709482220.004620538195870.1559094360810.0794798259441-0.00149760254222-0.171127155773-0.0766797232240.2503461620640.09014425720760.951001708528-0.249591551048-0.07921460442770.4694896145430.08068685066980.375596161652-17.449458459415.39930859316.9524460185
182.111445688450.4451358000580.7385123679271.398426702970.5707848492880.400614602225-0.04051426219010.1738157996540.23160979324-0.0423808964324-0.008019871551580.106605447458-0.2409841366890.01593464176970.070586203450.9450321372880.0185588759385-0.006573960063160.476952883535-0.1351646629410.380498393843-25.530897894518.702369632611.0906744648
192.804691037550.5463707995910.6641622820042.78532653742-0.0473415984673.526874655850.04117298544240.0418255265176-0.110332055078-0.009012853938-0.072490911714-0.3745193913730.149413969260.4038166747640.01395055731950.591668241774-0.01858022044490.01154685817020.31456963341-0.03316558728160.212803047128-17.88424160077.315663514999.45957473488
202.46433239197-0.2708918622781.258607127762.1034418123-1.024250942785.7456364006-0.06910902378210.0012620771542-0.0254844196475-0.01141597440930.1148613834230.09288915329040.0027352588587-0.100979420848-0.05543380020960.606789179573-0.2270469823540.05229339999880.3905898589970.06910685664630.219022352601-26.56795434172.575338276613.8905520606
211.294707390070.928322869052-0.2162298206251.095664686860.1889691752973.136205403890.0369116247799-0.02675127272350.120398581004-0.08812689859960.01974426722350.134776565762-0.185004083015-0.115212407728-0.03139792942160.7738088998540.00867566389576-0.0006805005584180.466062335309-0.1678675772420.227331813184-23.778947103310.961096399718.3463806406
220.3288325270050.228762586961-0.1019613635010.3845587027150.1653889040120.6013788405170.00708124717109-0.09644292212340.07450459016650.288858913327-0.0815820027774-0.206290155478-0.2934284488150.2983853452410.01845792357490.563363766178-0.0806994020245-0.1120920295690.185557774484-0.02538047640590.212036289367-19.23213756999.858402260975.74935483452
230.003729094681950.00164332672633-0.00235323803980.001011831226340.002992598033450.00818134131021-0.006101479407220.0511442300574-0.0507176125693-0.011049838366-0.04291083646690.07683208872090.109931042932-0.09362805840260.06171887481190.806365325976-0.295818791731-0.2176968788390.750081988974-0.01671390602470.549230507046-52.5578951304-26.9960872057-46.5236160383
241.172688137840.1618058631770.07960285289940.545101048227-0.2393683706790.1597524713270.0656005436236-0.2218083215940.1177356320160.148716630071-0.03640081114360.190095472223-0.158458781897-0.28083942285-0.05336734583060.90775770519-0.375270435203-0.07505981041490.74348019001-0.004459750768930.347093395115-53.1899974126-20.1659262053-44.0350093432
253.30365231624-0.642464235366-0.1744331237092.844500944920.4039150544753.654720137550.01680714938830.0112629470804-0.254895992864-0.02673945419280.0423980443535-0.08130472020930.4093735588230.196332611751-0.05761387941660.71036859989-0.212980678877-0.1840483968070.4349313327290.05424893803010.224677077236-42.3858742063-23.1796576645-40.6814576838
261.23302255495-0.10229615552-0.01809080873043.36505407313-0.08263137528972.797504077640.03701991177450.004509231274490.0450318475513-0.00239008621721-0.02886804901140.0617437416825-0.143150857967-0.0857417249427-0.01145052201270.720572015961-0.146821496022-0.0981569769810.1931488447140.06162226596090.291510688621-41.2580415002-12.9783748995-44.4453673149
270.1098406133250.01093886539220.02814327684590.00346530347599-0.02397464797510.6294150121820.05742464544370.03457333375790.0555052321571-0.1433658652150.01562536200590.1236024107560.00600146878623-0.270769885879-0.1577995525790.888525029837-0.323663703306-0.1693586374140.4271076145970.1398401745170.272691877258-48.2099037569-18.8632429836-42.7460218116
280.1092584841360.1841683664050.2074298202660.2988498801240.3332654967310.3769301431240.03644603134980.0143893132667-0.0420157676698-0.06742534750780.001366743392740.06416806842790.284279281144-0.186524397705-0.03158226578210.815366543946-0.281659612233-0.07609720591110.2619183132440.01971210890550.188614433608-43.6538119112-24.9864302798-38.1066422765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 47 )
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 95 )
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 113 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 5 )
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 11 )
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 22 )
11X-RAY DIFFRACTION11chain 'B' and (resid 23 through 47 )
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 57 )
13X-RAY DIFFRACTION13chain 'B' and (resid 58 through 71 )
14X-RAY DIFFRACTION14chain 'B' and (resid 72 through 86 )
15X-RAY DIFFRACTION15chain 'B' and (resid 87 through 95 )
16X-RAY DIFFRACTION16chain 'B' and (resid 96 through 113 )
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 19 )
18X-RAY DIFFRACTION18chain 'C' and (resid 20 through 34 )
19X-RAY DIFFRACTION19chain 'C' and (resid 35 through 53 )
20X-RAY DIFFRACTION20chain 'C' and (resid 54 through 69 )
21X-RAY DIFFRACTION21chain 'C' and (resid 70 through 93 )
22X-RAY DIFFRACTION22chain 'C' and (resid 94 through 128 )
23X-RAY DIFFRACTION23chain 'D' and (resid 5 through 14 )
24X-RAY DIFFRACTION24chain 'D' and (resid 15 through 34 )
25X-RAY DIFFRACTION25chain 'D' and (resid 35 through 53 )
26X-RAY DIFFRACTION26chain 'D' and (resid 54 through 69 )
27X-RAY DIFFRACTION27chain 'D' and (resid 70 through 108 )
28X-RAY DIFFRACTION28chain 'D' and (resid 109 through 128 )

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