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- PDB-8u17: The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long boun... -

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Basic information

Entry
Database: PDB / ID: 8u17
TitleThe ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide
Components
  • DNA damage-binding protein 1
  • Protein cereblon
  • Sal-like protein 4
KeywordsLIGASE / complex / glue
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / embryonic limb morphogenesis / UV-damage excision repair / ventricular septum development / inner cell mass cell proliferation ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / embryonic limb morphogenesis / UV-damage excision repair / ventricular septum development / inner cell mass cell proliferation / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / viral release from host cell / cullin family protein binding / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / heterochromatin / proteasomal protein catabolic process / positive regulation of gluconeogenesis / Regulation of PTEN gene transcription / neural tube closure / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / protein ubiquitination / DNA repair / intracellular membrane-bounded organelle / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) ...: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / PUA-like superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
S-Pomalidomide / DNA damage-binding protein 1 / Protein cereblon / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsClifton, M.C. / Ma, X. / Ornelas, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon.
Authors: Ma, X. / Leon, B. / Ornelas, E. / Dovala, D. / Tandeske, L. / Luu, C. / Pardee, G. / Widger, S. / Solomon, J.M. / Beckwith, R.E.J. / Moser, H. / Clifton, M.C. / Wartchow, C.A.
History
DepositionAug 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein cereblon
B: DNA damage-binding protein 1
C: Sal-like protein 4
D: Protein cereblon
E: DNA damage-binding protein 1
F: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,95014
Polymers292,0116
Non-polymers9398
Water00
1
A: Protein cereblon
B: DNA damage-binding protein 1
C: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4757
Polymers146,0063
Non-polymers4694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-41 kcal/mol
Surface area51430 Å2
MethodPISA
2
D: Protein cereblon
E: DNA damage-binding protein 1
F: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4757
Polymers146,0063
Non-polymers4694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-42 kcal/mol
Surface area51960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.077, 151.660, 195.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein cereblon


Mass: 42971.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#2: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 93347.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#3: Protein Sal-like protein 4


Mass: 9687.075 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SALL4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJQ4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-Y70 / S-Pomalidomide


Mass: 273.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium malonate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→49.9 Å / Num. obs: 63326 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0631 / Rpim(I) all: 0.08 / Rrim(I) all: 0.282 / Rsym value: 0.212 / Χ2: 1.04 / Net I/σ(I): 7.4 / Num. measured all: 788438
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 12.3 % / Rmerge(I) obs: 9.9 / Num. unique obs: 4418 / CC1/2: 0.317 / Rpim(I) all: 3.431 / Rrim(I) all: 12.093 / Χ2: 1.01

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→49.9 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3456 3073 5.06 %
Rwork0.3048 --
obs0.3069 60745 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16987 0 46 0 17033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217377
X-RAY DIFFRACTIONf_angle_d0.5123759
X-RAY DIFFRACTIONf_dihedral_angle_d4.3272523
X-RAY DIFFRACTIONf_chiral_restr0.0442793
X-RAY DIFFRACTIONf_plane_restr0.0053138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.7901490.662985X-RAY DIFFRACTION36
3.15-3.20.47411250.46252462X-RAY DIFFRACTION92
3.2-3.260.46651410.40932661X-RAY DIFFRACTION98
3.26-3.310.43521490.40622674X-RAY DIFFRACTION100
3.31-3.380.41491510.42472687X-RAY DIFFRACTION100
3.38-3.450.49981430.42092694X-RAY DIFFRACTION100
3.45-3.520.46121360.38272697X-RAY DIFFRACTION100
3.52-3.60.3951380.37212723X-RAY DIFFRACTION100
3.6-3.690.50361420.46122644X-RAY DIFFRACTION99
3.69-3.790.42031320.39812700X-RAY DIFFRACTION99
3.79-3.910.47391540.41032672X-RAY DIFFRACTION99
3.91-4.030.43081190.37952664X-RAY DIFFRACTION98
4.03-4.180.34391220.30952707X-RAY DIFFRACTION99
4.18-4.340.34011610.28552701X-RAY DIFFRACTION99
4.34-4.540.30591350.26362688X-RAY DIFFRACTION99
4.54-4.780.35851430.25352712X-RAY DIFFRACTION99
4.78-5.080.31711580.2422689X-RAY DIFFRACTION99
5.08-5.470.3331530.26552704X-RAY DIFFRACTION99
5.47-6.020.28581430.27392748X-RAY DIFFRACTION100
6.02-6.890.29991700.26912760X-RAY DIFFRACTION100
6.89-8.670.27351660.27482769X-RAY DIFFRACTION100
8.67-49.90.25121430.2212931X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1956-2.2493-1.26881.0692-0.63535.06590.69820.9515-0.3761-1.1867-0.58790.1394-0.0557-0.62570.02811.95680.47690.02760.7434-0.24650.7799-37.45228.2316-43.778
21.53150.06960.27492.1328-0.05720.05280.4347-0.34070.68410.0278-0.65471.5552-0.8255-0.64480.16991.39960.61260.53760.9467-0.381.0825-37.516140.6161-35.6814
38.5839-0.5350.62417.5194-2.219.21090.5037-0.00370.6467-0.3231-0.49881.08080.67740.1751-0.01971.16530.19830.28080.5875-0.14320.8207-35.907134.6306-36.7573
42.505-1.2833-0.45948.51855.55346.03670.94620.73880.2273-1.9159-1.02241.1341-0.9692-0.87240.32231.69320.53080.16730.9476-0.23610.5998-37.523835.1363-41.3983
51.5651-2.3167-1.16637.90560.35761.21530.3161-0.23080.165-0.4654-0.8695-0.1770.1663-0.35760.61311.39640.24360.11670.7606-0.06110.665-21.0084-0.031-43.3691
62.20520.22190.24374.83622.2672.07130.0584-0.10910.2971-0.1393-0.4175-0.21020.16710.12490.09271.39870.20710.47140.67050.08760.5445-16.291213.7247-43.6029
70.83590.29080.70764.8527-0.23610.62480.63220.23650.6559-0.1372-0.9953-0.7329-0.42630.4567-0.22842.09990.25380.75210.48020.22591.0722-14.282534.0682-45.4126
81.04660.6560.51635.3593-0.07770.28930.59360.0167-0.14650.4198-0.8659-1.6259-0.09380.43450.57771.9806-0.08560.75580.46010.49541.514-8.622938.2835-42.052
92.4343-0.60420.38240.1662-0.194.51340.19940.2695-0.7237-0.7254-0.55771.13570.5176-0.50380.12611.87780.0798-0.41350.7864-0.35990.9482-37.9715-24.6314-48.6257
105.67750.0209-0.29485.019-0.61434.19630.2079-0.64080.5638-0.145-0.47060.5973-0.6684-0.56740.27090.7686-0.0077-0.0490.5512-0.1870.5467-39.769-13.9469-34.0353
112.186-1.72960.57484.5691-1.13873.2095-0.2282-0.3904-0.61630.9005-0.2730.1211-0.4717-0.16760.2381.0281-0.60370.27250.65020.03510.6519-25.9705-16.1734-22.4611
121.61530.2842-1.52781.7973-1.08276.68230.30020.0066-0.4284-1.36-0.5293-0.2809-0.2246-0.06470.2091.1938-0.0110.12350.4642-0.06760.5889-18.9382-28.0126-42.1434
131.64780.2708-0.36550.8895-0.31750.90020.50240.5547-0.2122-1.0514-0.396-0.21060.10580.5190.23992.54690.43310.71460.70050.21420.8063-6.6737-12.1454-63.9377
142.118-0.2453-0.37171.0439-0.49171.2076-0.18520.70320.3002-1.1071-0.5365-0.7179-0.5154-0.1314-0.61723.52250.81980.53880.63390.59670.942-14.49245.9696-71.0475
151.15490.5295-1.20730.2402-0.54421.22290.06460.39290.3921-0.2270.09690.1479-0.6843-0.59430.04182.89290.7818-0.2081.035-0.25460.4459-32.6374-1.0334-67.1689
163.3917-0.361-1.58940.1722-0.23353.7768-0.0221-0.45840.5633-0.9614-0.21320.7236-0.0935-0.78550.25162.06370.264-0.58240.838-0.43791.2334-47.7368-11.7055-64.84
176.5968-3.5261-4.41322.9363.7335.7561-0.29610.72180.4178-1.10040.5296-0.2073-0.3691-0.8977-0.14112.85780.31070.34620.77140.10030.9009-29.505861.6603-35.5882
184.28842.07744.20782.20771.97284.19090.4807-1.22521.9783-0.6163-0.2929-1.0229-4.814-0.4669-0.21831.8663-0.00280.07531.3878-0.17611.6449-18.288564.1309-34.7863
190.3501-1.1417-0.40964.15750.74881.23510.30430.15070.6367-0.17010.27070.04260.68120.0526-0.38132.26560.24750.60250.47570.20141.8456-18.654454.7406-47.5752
201.43541.68010.61465.73511.49182.33790.1926-0.20160.6383-0.6168-1.03562.102-0.873-0.43560.82281.4360.028-0.50840.686-0.16760.9314.913533.577712.6424
211.5620.93340.12735.68281.59971.94670.2230.07070.2119-0.7570.1266-0.7555-1.29670.4615-0.35051.4321-0.10270.03440.6489-0.02930.667633.227526.0310.8925
22222222-1.147410.3294-0.3036-4.0333-0.4116-23.5568-2.68280.1811.56180.9187-0.3424-0.10011.7325-0.0131.124832.637529.2146-21.5224
232.2756-0.40020.10851.56010.43691.6230.0071-0.2336-0.8827-0.0642-0.39650.80910.33420.2504-0.3430.24240.1318-0.70460.4638-0.03871.04729.2017-21.3419.5892
243.740.4734-0.44883.8311-0.43463.02260.0492-0.52480.14490.97310.12610.2079-0.38330.194-0.15110.2786-0.0815-0.1920.6089-0.01310.593217.632-10.616522.8849
252.9297-0.4778-0.39513.05571.33946.2404-0.0211-0.7833-0.01321.01790.1317-0.3655-1.08280.4502-0.23471.1515-0.0532-0.3110.67640.0450.518633.9877-14.91924.5093
262.1746-0.47952.0572.2344-1.87335.3142-0.09130.2108-0.3473-0.6064-0.4141-0.1250.46320.35440.1290.75010.0563-0.32760.4446-0.11250.614328.1093-24.89793.3626
272.02190.54750.55651.37590.18141.92130.14330.78190.0583-1.8728-0.25420.2433-0.44030.31750.16162.08090.1823-0.35550.9058-0.09190.669422.5106-0.5616-21.1237
281.6267-0.69460.04242.1559-1.01451.11060.0174-0.0479-0.17560.1787-0.03911.17-0.1094-0.27030.21270.33070.0198-0.98230.5186-0.28551.5492-2.9001-4.1488-2.7855
292.7532-2.9239-1.60387.093-2.3365.0493-0.3719-0.84671.24410.09420.7389-0.1123-1.48280.814-0.40362.2235-0.1293-0.26560.8604-0.09150.774227.731364.692414.4639
308.69946.0454-4.18235.4214-1.8953.4403-0.822.31632.5776-2.31532.39193.8930.869-1.203-1.56182.873-0.34190.11630.8863-0.03842.25834.851262.90673.3665
311.86871.6729-1.05912.361-1.54691.0170.13150.45011.1568-0.85940.1425-1.0893-0.36190.1087-0.14512.3045-0.1296-0.14360.57570.22811.408231.951557.07091.3866
323.31084.05113.69655.08944.53954.1286-0.13380.65841.3186-2.63550.45520.4184-0.7880.4021-0.32413.5427-0.31870.02850.72720.10171.556925.796657.6908-2.7652
330.16640.7593-0.25793.7008-1.75971.8439-2.09111.9016-1.7091-4.660.9869-2.77421.09830.89851.11842.7384-0.3184-0.25221.4113-0.26821.900820.102648.8950.2242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 179 )
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 291 )
7X-RAY DIFFRACTION7chain 'A' and (resid 292 through 396 )
8X-RAY DIFFRACTION8chain 'A' and (resid 397 through 427 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 84 )
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 186 )
11X-RAY DIFFRACTION11chain 'B' and (resid 187 through 248 )
12X-RAY DIFFRACTION12chain 'B' and (resid 249 through 374 )
13X-RAY DIFFRACTION13chain 'B' and (resid 375 through 845 )
14X-RAY DIFFRACTION14chain 'B' and (resid 846 through 958 )
15X-RAY DIFFRACTION15chain 'B' and (resid 959 through 1036 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1037 through 1139 )
17X-RAY DIFFRACTION17chain 'C' and (resid 381 through 401 )
18X-RAY DIFFRACTION18chain 'C' and (resid 402 through 406 )
19X-RAY DIFFRACTION19chain 'C' and (resid 407 through 434 )
20X-RAY DIFFRACTION20chain 'D' and (resid 71 through 199 )
21X-RAY DIFFRACTION21chain 'D' and (resid 200 through 427 )
22X-RAY DIFFRACTION22chain 'D' and (resid 428 through 428 )
23X-RAY DIFFRACTION23chain 'E' and (resid 2 through 84 )
24X-RAY DIFFRACTION24chain 'E' and (resid 85 through 194 )
25X-RAY DIFFRACTION25chain 'E' and (resid 195 through 248 )
26X-RAY DIFFRACTION26chain 'E' and (resid 249 through 385 )
27X-RAY DIFFRACTION27chain 'E' and (resid 386 through 964 )
28X-RAY DIFFRACTION28chain 'E' and (resid 965 through 1139 )
29X-RAY DIFFRACTION29chain 'F' and (resid 381 through 406 )
30X-RAY DIFFRACTION30chain 'F' and (resid 407 through 411 )
31X-RAY DIFFRACTION31chain 'F' and (resid 412 through 421 )
32X-RAY DIFFRACTION32chain 'F' and (resid 422 through 431 )
33X-RAY DIFFRACTION33chain 'F' and (resid 432 through 436 )

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