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- PDB-7mrk: Chicken CNTN4 APP complex -

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Basic information

Entry
Database: PDB / ID: 7mrk
TitleChicken CNTN4 APP complex
Components
  • Amyloid-beta A4 protein
  • Contactin-4
KeywordsCELL ADHESION / Ig superfamily / amyloid precursor protein
Function / homology
Function and homology information


Golgi-associated vesicle / transition metal ion binding / axon guidance / serine-type endopeptidase inhibitor activity / heparin binding / nervous system development / cell adhesion / apoptotic process / Golgi apparatus / cell surface ...Golgi-associated vesicle / transition metal ion binding / axon guidance / serine-type endopeptidase inhibitor activity / heparin binding / nervous system development / cell adhesion / apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / nucleus / plasma membrane
Similarity search - Function
Amyloid-beta precursor protein / Basigin-like / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...Amyloid-beta precursor protein / Basigin-like / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Contactin 4 / Amyloid-beta A4 protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBouyain, S. / Karuppan, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R15NS108371-01 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Members of the vertebrate contactin and amyloid precursor protein families interact through a conserved interface.
Authors: Karuppan, S.J. / Vogt, A. / Fischer, Z. / Ladutska, A. / Swiastyn, J. / McGraw, H.F. / Bouyain, S.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
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

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Assembly

Deposited unit
A: Amyloid-beta A4 protein
B: Contactin-4
C: Amyloid-beta A4 protein
D: Contactin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3885
Polymers108,2814
Non-polymers1061
Water9,044502
1
A: Amyloid-beta A4 protein
B: Contactin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2473
Polymers54,1412
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-5 kcal/mol
Surface area18600 Å2
MethodPISA
2
C: Amyloid-beta A4 protein
D: Contactin-4


Theoretical massNumber of molelcules
Total (without water)54,1412
Polymers54,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.450, 65.510, 158.294
Angle α, β, γ (deg.)90.000, 92.919, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein Amyloid-beta A4 protein


Mass: 20582.480 Da / Num. of mol.: 2 / Fragment: E1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DGJ7
#2: Protein Contactin-4 / / CNTN4


Mass: 33558.238 Da / Num. of mol.: 2 / Fragment: domains FN1-FN3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CNTN4 / Production host: Escherichia coli (E. coli) / References: UniProt: F1P3U6
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 150 mM (NH4)2SO4, 50 mM Na-cacodylate pH 6.5, 30% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→64.14 Å / Num. obs: 82428 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Rrim(I) all: 0.111 / Net I/σ(I): 10
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4511 / CC1/2: 0.805 / Rpim(I) all: 0.326 / Rrim(I) all: 0.839 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KTM, 5E4S
Resolution: 2.05→32.41 Å / SU ML: 0.2393 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.7305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 1938 2.42 %
Rwork0.1834 78072 -
obs0.1844 80010 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 7 508 6837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316493
X-RAY DIFFRACTIONf_angle_d0.59058853
X-RAY DIFFRACTIONf_chiral_restr0.0483979
X-RAY DIFFRACTIONf_plane_restr0.0041152
X-RAY DIFFRACTIONf_dihedral_angle_d12.25852367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.32331260.25455186X-RAY DIFFRACTION90.99
2.1-2.160.24211310.22285319X-RAY DIFFRACTION92.94
2.16-2.220.24151320.20625389X-RAY DIFFRACTION94.02
2.22-2.290.2431500.20335400X-RAY DIFFRACTION94.63
2.29-2.380.22531190.19695564X-RAY DIFFRACTION96.24
2.38-2.470.25971370.2055513X-RAY DIFFRACTION96.47
2.47-2.580.25121490.20835586X-RAY DIFFRACTION97.47
2.58-2.720.2441380.21325660X-RAY DIFFRACTION98.29
2.72-2.890.24811410.21355663X-RAY DIFFRACTION98.72
2.89-3.110.25641410.20635778X-RAY DIFFRACTION99.51
3.11-3.420.23371450.18815745X-RAY DIFFRACTION99.8
3.42-3.920.22951450.17015753X-RAY DIFFRACTION99.76
3.92-4.940.18961440.14555819X-RAY DIFFRACTION99.62
4.94-32.410.18651400.1665697X-RAY DIFFRACTION95.83
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)
17.013751346964.03237515772.724087791962.940923322140.9395849769172.35060984815-0.4355517902750.05400597747580.430031087945-0.3099110334040.4306276460390.666361278428-0.664026211278-0.288794911632-0.08775463198880.5017807530470.0813094731997-0.0004299206594930.3575452758-0.006193317926920.45121474650813.835062989485.793296127956.8389484253
25.893008032220.449308904367-1.433094609249.02388625593-0.2563933538065.56073445932-0.29594689445-0.4644045823590.8938954843420.2214800370040.3808035173530.59714283335-0.993984343741-0.431153485269-0.0591566121010.53175988320.0297243290838-0.04111189806940.31426228249-0.1117816602120.52091431652116.186661478589.202216016760.2417183292
32.796360293752.026650771852.575889855292.91264873153.210778014183.702187026770.02293078205180.3271211276111.12657653055-0.886679842240.218235239681-0.073853515527-1.205607164640.7652560516460.002702795725740.653351855712-0.0522282403692-0.00863214012760.359688301349-0.04693751815390.48057550181923.398947530988.271863177952.315951335
43.432315814220.8151893683590.2487311731925.797790696470.7161354298062.49659001625-0.141017503518-0.2217633442050.1192158160090.08751954642940.119788489679-0.0997982962507-0.4274391978490.0877292312755-0.01981146872150.389337388108-0.02533401765170.05044611126390.327099148738-0.1045864589280.32797418026821.299024967180.734928704357.6103923605
55.56744154961-0.1586901738320.2824968841112.15297392269-0.2590167565846.94849003186-0.1723963445990.3154730565072.074359240861.14943400518-0.517511357351.83795464136-1.69045219522-0.708270145793-0.209382615610.7693772403120.1333639097420.03391016441870.720811627186-0.1499689682271.092124339845.9918501245793.541367447360.5564861356
62.237457613320.0585562635856-0.04144337541224.989965931220.002817094360745.09483730825-0.101335908642-0.5424701507841.08303275932-0.05052164798510.1919273032760.456999711761-0.480324793177-0.253240363277-0.02083159415350.3643016547650.02922879442510.002185046919030.267077860052-0.0670540645910.35153956470716.413611468979.7612801256.1270251478
73.736777997583.92745994382-2.045432585954.25380891922-2.743392485536.01828632228-0.265374860706-0.710511788014-0.427285638918-0.344907512548-0.0555290214484-0.7439593567810.385172601070.6099301815370.154885567440.3359506570550.0195533031520.03358185321910.362488563952-0.08641462953680.34713158544725.17643258363.604500371259.6644447856
82.80497359569-2.201173765420.4948579778846.09746955411-3.233742500838.632009158720.2307708863880.623004141543-0.156650717035-1.0132397734-0.448343805736-0.2788679987170.2741827166110.4382001404750.2634717158840.4067595864120.0362076453612-0.006836204081870.470594656143-0.1497987014750.28955916697626.668102147363.48920268745.2801200713
92.784522664272.24283006807-1.49495040348.51894717095-4.66645126843.162604827490.04468161666410.423187298737-0.637080615417-0.5526755472680.1413213845160.3414012125850.369041336852-0.36001393332-0.1410837526370.303394442426-0.0391400919137-0.07182885339690.352430470205-0.1305439209430.35464939768316.876688484162.198664343746.4431526642
103.40896949321.319399098470.4439354850018.03866054009-0.8529291009343.99217824430.2437772183530.0672670238575-0.3294267607410.114731646035-0.1572058532260.3382235108540.0691821708677-0.0232423103814-0.1202899328640.219377610333-0.00505975406849-0.01112110179170.272853746502-0.1154455070820.2451887552321.5077231464.748886430651.1851316554
117.35274723758-2.54950725593-0.9476911901993.268288516951.320533982972.401102537680.01634795628630.174751283623-0.134259560355-0.0687121852001-0.0505966309822-0.2706172055160.1947379356940.0735174993111-0.002216960119770.256768095294-0.00466788926990.07448628140030.205103082321-0.003370880053950.31339680758961.819215950739.936749353536.2618794609
128.12300522943-3.11361681207-2.938865776173.447695913171.355649811772.763942588050.07273491937410.07959026213210.565307836545-0.09366188307090.0937044287876-0.3782017446160.00704295335525-0.0676513423854-0.0749134870610.213569169766-0.007686412159930.01931352705630.208977395705-0.03286813212310.29568583962957.785517592245.682636261638.4170653131
132.51242392258-0.812435730865-0.98623593532.943357643450.9627765968954.982141829140.00162440187899-0.6216964030160.4216528739030.4916224781910.225955782541-0.5068035194510.0724977592580.379862537659-0.1825735767620.3043395636570.0500731271378-0.07050838951520.419796967546-0.1085631522650.28477721311337.010581681760.225028511761.0583768222
143.22137146943-0.355662186365-0.5619269977542.0566548313-0.4102558231071.20495525293-0.210617806399-0.726423137570.5245982638450.8158081374280.0722649170796-0.0198295996156-0.3140106208280.4936499433230.08286791155290.5073513234460.0407535819798-0.0633183302040.532559913587-0.1419791724770.2859061550233.190201255661.680624219865.7658906872
157.97347927187-0.3725116370960.8755267448518.041105466960.669307995497.11926268359-0.533881171684-0.864037748326-0.9724501626860.6612679808660.268926759601-0.2681722499640.3081778326990.2210074572010.3468174440940.7082075666290.2489685114570.05423192074080.5052392396760.09711167654640.541375495826109.16082402924.894697922562.075099227
165.83225178997-0.465079338544-0.8619837257469.12056434509-4.782159438773.56965688939-0.7083867826260.481982938661-1.87113765591-0.5186308088450.1779311123870.4395264548111.595686980490.07079357666240.1044091986920.9078791562280.02462837304770.1353013801610.339070696671-0.05665446322190.726673372655104.70460582920.256579305852.7743302929
176.14599078422-0.5796863652341.518089334446.94415636317-1.335886267282.630339188850.0353279947191-0.360133475223-0.6277944320080.442615590638-0.0739713114309-0.1506421328750.7227546683250.4338294053240.167840675190.657226480810.150898185948-0.01618480379360.396951304150.00536117457420.402346084596108.83595638625.246288838258.8991060151
185.63973189105-4.942869565471.033168239734.59678163003-0.6557022938810.39835930405-0.282461907763-0.70213567636-0.4674023192760.2596556136360.172315735465-0.07784503732390.2641860433680.06027215845410.1057791176270.5323547448340.157812334571-0.01516891150890.4400538230240.01107067564170.428236018756107.80726596630.983869071356.5683583353
198.192820036383.973975070850.002344222990593.306716774553.063607118237.1716997910.188510624978-0.3767186393840.03969361680110.341216041149-0.2107095524970.134317039036-0.182105226797-0.01845240856130.03873620580650.2517125350950.0336281485383-0.06460143258910.2314417012160.08283741936320.22016344761899.12890947747.307669323559.9674968527
203.83864328902-2.7435150112-1.240820520354.860032442511.867064822965.939017933970.3617977132390.814281040195-0.055181996146-0.978521754115-0.413550673459-0.0135540951082-0.263327519153-0.5818260599270.1110719260850.3800654371910.017173846598-0.0208519854310.4694701818930.07590122116260.24736154803397.695213037247.279675328945.5378725315
215.127263277771.992330946470.3824562869749.88064305985.447825473584.674817322850.04741241740090.454405104070.500976555147-0.3593625039120.302880830747-0.300276302801-0.3690180217680.616096621307-0.342822546040.320701187155-0.01487787564030.05932334082410.3784563022740.05648655729310.271830897854107.43644541248.563014912746.7400992482
224.864954232551.87989806921-0.8670642177989.607112597760.641086228324.648001920050.194481642932-0.01795738390570.03117676535260.127194865352-0.135078302538-0.3510802056520.07619745883140.200311561049-0.07937171794820.154463345690.0201570814423-0.01310630690760.2436655110580.05499458228710.16390867012102.75613867746.067235562351.4883756843
237.66006966911-3.098587884041.072968526322.68139565309-1.317525459011.60564702690.0807921275180.2077299887460.0504462396461-0.0658722634614-0.02293941933270.493525162011-0.216324267237-0.0783818961726-0.05546065967350.316218094718-0.00114742041557-0.1020180071290.2491358123810.06544990708380.50801700161663.365609431869.621746881537.0286487814
243.86278387240.0331932992573.72730922241.90806428778-1.620326578686.2672545249-0.2510168173390.184889562163-0.0007766892913530.0811859428785-0.03495863611940.328158439338-0.07872073267290.3626336508910.3085920738880.2824650335720.08626941301360.01843132680840.2446887518160.02202256453260.37454768768978.439996113858.787190586846.715623904
252.85958258363-0.380721755303-0.04056276368753.00550291642-0.8360006293954.928836873420.051815709246-0.503952387657-0.2799996507640.5279983529130.1157689368060.3787294979810.130323679286-0.148586822085-0.2327054878010.3306420691970.006368696138610.04907001273130.3141973904690.1267220527470.2814012455289.49579041748.492648118763.6672277296
260.9755501152650.663996083063-0.08740982824611.98918194265-4.273122900154.574161550060.1569772917-0.345197968463-0.07516116604390.165943763776-0.1105935714780.1802278322920.3073937143090.375302761954-0.03618997463030.7546428295660.0844620793830.108005064720.5126271177170.1741283046640.29300187954289.274341845445.898220147473.5878145549
276.1661528948-1.34747502718-3.075319117911.481401062791.599014114796.15092058001-0.05752653495230.4360967275630.0609503341985-0.303557229885-0.2925966536390.397399500093-0.344120101197-0.1977278704340.310884767630.519663477250.04538362895260.03809533254470.3358241345130.08658667494810.37073174461177.423639524931.056395386899.1037057313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 109 )
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 119 )
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 146 )
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 161 )
10X-RAY DIFFRACTION10chain 'A' and (resid 162 through 189 )
11X-RAY DIFFRACTION11chain 'B' and (resid 595 through 658 )
12X-RAY DIFFRACTION12chain 'B' and (resid 659 through 698 )
13X-RAY DIFFRACTION13chain 'B' and (resid 699 through 759 )
14X-RAY DIFFRACTION14chain 'B' and (resid 760 through 798 )
15X-RAY DIFFRACTION15chain 'C' and (resid 30 through 54 )
16X-RAY DIFFRACTION16chain 'C' and (resid 55 through 76 )
17X-RAY DIFFRACTION17chain 'C' and (resid 77 through 109 )
18X-RAY DIFFRACTION18chain 'C' and (resid 110 through 119 )
19X-RAY DIFFRACTION19chain 'C' and (resid 120 through 133 )
20X-RAY DIFFRACTION20chain 'C' and (resid 134 through 146 )
21X-RAY DIFFRACTION21chain 'C' and (resid 147 through 161 )
22X-RAY DIFFRACTION22chain 'C' and (resid 162 through 189 )
23X-RAY DIFFRACTION23chain 'D' and (resid 596 through 688 )
24X-RAY DIFFRACTION24chain 'D' and (resid 689 through 708 )
25X-RAY DIFFRACTION25chain 'D' and (resid 709 through 781 )
26X-RAY DIFFRACTION26chain 'D' and (resid 782 through 809 )
27X-RAY DIFFRACTION27chain 'D' and (resid 810 through 900 )

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