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- PDB-4wfc: Structure of the Rrp6-Rrp47 interaction -

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Basic information

Entry
Database: PDB / ID: 4wfc
TitleStructure of the Rrp6-Rrp47 interaction
Components
  • Exosome complex exonuclease RRP6
  • Exosome complex protein LRP1
KeywordsHYDROLASE / Rrp6-Rrp47 complex / nuclear exosome / RNA degradation / RNA processing
Function / homology
Function and homology information


nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / U4 snRNA 3'-end processing ...nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / rRNA primary transcript binding / RNA catabolic process / regulation of telomere maintenance / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / enzyme regulator activity / double-stranded RNA binding / regulation of gene expression / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / double-stranded DNA binding / single-stranded RNA binding / nucleotide binding / protein-containing complex binding / nucleolus / DNA binding / RNA binding / nucleus
Similarity search - Function
Exosome-associated factor Rrp47/DNA strand repair C1D / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / Helicase and RNase D C-terminal / HRDC domain / HRDC domain ...Exosome-associated factor Rrp47/DNA strand repair C1D / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Exosome complex protein LRP1 / Exosome complex exonuclease RRP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsSchuch, B. / Conti, E.
Funding support Germany, 3items
OrganizationGrant numberCountry
European Research CouncilAdvanced Investigator Grant 294371
Marie CurieITN RNPnet
German Research FoundationSFB646, SFB1035, GRK1721, FOR1680, CIPSM Germany
CitationJournal: Embo J. / Year: 2014
Title: The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase.
Authors: Schuch, B. / Feigenbutz, M. / Makino, D.L. / Falk, S. / Basquin, C. / Mitchell, P. / Conti, E.
History
DepositionSep 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / software / struct_conf / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _software.classification / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_site_gen.auth_seq_id
Revision 2.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exosome complex exonuclease RRP6
B: Exosome complex protein LRP1
C: Exosome complex exonuclease RRP6
D: Exosome complex protein LRP1
E: Exosome complex exonuclease RRP6
F: Exosome complex protein LRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,99610
Polymers84,6126
Non-polymers3844
Water8,341463
1
A: Exosome complex exonuclease RRP6
B: Exosome complex protein LRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3964
Polymers28,2042
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-75 kcal/mol
Surface area12690 Å2
MethodPISA
2
C: Exosome complex exonuclease RRP6
D: Exosome complex protein LRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3964
Polymers28,2042
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-71 kcal/mol
Surface area10990 Å2
MethodPISA
3
E: Exosome complex exonuclease RRP6
F: Exosome complex protein LRP1


Theoretical massNumber of molelcules
Total (without water)28,2042
Polymers28,2042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-42 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.397, 98.397, 208.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

21B-318-

HOH

31B-408-

HOH

41B-412-

HOH

51C-400-

HOH

61D-313-

HOH

71D-392-

HOH

81D-396-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
32chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSchain AAA3 - 1067 - 110
21ASPASPLYSLYSchain CCC7 - 10611 - 110
12ASPASPASPASPchain BBB3 - 1203 - 120
22GLUGLUGLUGLUchain DDD5 - 1025 - 102
32TYRTYRGLUGLUchain FFF10 - 10210 - 102

NCS ensembles :
ID
1
2

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Components

#1: Protein Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 12862.192 Da / Num. of mol.: 3 / Fragment: UNP residues 1-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP6, UNC733, YOR001W / Production host: Escherichia coli (E. coli)
References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein Exosome complex protein LRP1 / Like an rRNA processing protein 1 / Yeast C1D domain-containing protein / rRNA processing protein 47


Mass: 15341.698 Da / Num. of mol.: 3 / Fragment: UNP residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LRP1, RRP47, YC1D, YHR081W / Production host: Escherichia coli (E. coli) / References: UniProt: P38801
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 1.8 M ammonium sulfate, 125 mM sodium chloride, 100 mM sodium cacodylate pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.35→88.95 Å / Num. obs: 43613 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 41.65 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 16.6 / Num. measured all: 562480
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible allRmerge(I) obs
2.35-2.4312.71.65223141070.5860.56297.8
9.09-88.9510.672.5949289910.00899.80.025

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Processing

Software
NameVersionClassification
XDS0.3.5data reduction
PHENIX(phenix.refine: 1.9_1692)refinement
Aimlessdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: SAD
Starting model: The structure was solved with data from a Ta6Br14 soaked crystal at low resolution (5.2A) by SAD with SHELX and HKL2MAP using the anomalous Ta signal. Identifiable alpha-helices were ...Starting model: The structure was solved with data from a Ta6Br14 soaked crystal at low resolution (5.2A) by SAD with SHELX and HKL2MAP using the anomalous Ta signal. Identifiable alpha-helices were manually placed and used as a starting model for SAD-MR by exploiting the anomalous Se signal from Se-Met derivatised crystal,using the program Phenix Autosol. The structure was finally modelled and refined using the natived data submitted.

Resolution: 2.35→71.479 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 4074 5 %
Rwork0.1837 77424 -
obs0.1857 43544 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.95 Å2 / Biso mean: 65.5484 Å2 / Biso min: 25.34 Å2
Refinement stepCycle: final / Resolution: 2.35→71.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 20 463 4793
Biso mean--109.56 63.93 -
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084363
X-RAY DIFFRACTIONf_angle_d1.0385870
X-RAY DIFFRACTIONf_chiral_restr0.044692
X-RAY DIFFRACTIONf_plane_restr0.005752
X-RAY DIFFRACTIONf_dihedral_angle_d13.9031628
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A842X-RAY DIFFRACTION7.071TORSIONAL
12C842X-RAY DIFFRACTION7.071TORSIONAL
21B1375X-RAY DIFFRACTION7.071TORSIONAL
22D1375X-RAY DIFFRACTION7.071TORSIONAL
23F1375X-RAY DIFFRACTION7.071TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3462-2.37380.36241510.33232481263294
2.3738-2.40280.2811260.287527262852100
2.4028-2.43320.27731320.281726432775100
2.4332-2.46520.27441680.265826702838100
2.4652-2.4990.29061340.26626622796100
2.499-2.53470.26281220.248427282850100
2.5347-2.57250.23841520.244226422794100
2.5725-2.61270.2791170.246826972814100
2.6127-2.65550.29221420.238326992841100
2.6555-2.70130.25451410.240126362777100
2.7013-2.75050.25751420.226427002842100
2.7505-2.80340.27181430.230526822825100
2.8034-2.86060.27741430.221526342777100
2.8606-2.92280.23631400.199226792819100
2.9228-2.99080.22351410.195726842825100
2.9908-3.06560.24231350.189926782813100
3.0656-3.14850.25111490.177526802829100
3.1485-3.24110.18781410.1626832824100
3.2411-3.34570.22741370.165126592796100
3.3457-3.46530.18241350.149226812816100
3.4653-3.6040.18561440.146426792823100
3.604-3.76810.18361380.140827112849100
3.7681-3.96670.19561400.136126472787100
3.9667-4.21520.18951450.149626702815100
4.2152-4.54060.1711450.135226532798100
4.5406-4.99740.20031490.145726992848100
4.9974-5.72030.23691380.193626712809100
5.7203-7.20590.24861410.228426802821100
7.2059-71.5120.23151430.185726702813100
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)
10.00470.00010.0044-0.0011-0.00210.0092-0.4572-0.43980.04630.42480.20080.01830.0553-0.16150.00061.2594-0.0369-0.34741.39350.26330.968953.1506-24.249339.3122
20.15550.05630.22830.6405-0.26350.5815-0.2295-1.1163-0.24960.42070.14060.0477-0.12250.59-0.00070.6115-0.0358-0.00480.4475-0.06440.428443.044-18.147539.4707
30.96070.6180.80731.41520.13970.89490.3677-0.45440.57760.0645-0.05280.2324-1.1559-0.24470.00040.89250.08990.12850.5061-0.05710.626934.9762-7.274334.9076
40.16460.04260.02630.02920.02770.0304-0.71490.5720.6203-0.01310.4387-0.1697-0.30060.25620.00220.8207-0.075-0.12680.8078-0.03620.7445.1483-15.09319.1902
51.209-0.1090.94841.0323-0.17720.79940.4408-0.72570.41240.29510.02010.0263-1.18250.7591-0.00160.8859-0.09070.08250.5133-0.13020.600544.4173-10.27339.9311
60.34970.36810.38653.20730.09281.73430.0711-0.01960.057-0.0094-0.0476-0.1796-0.26060.03770.00030.4329-0.0143-0.01470.3012-0.00890.319344.7582-22.718525.1544
70.23450.2464-0.30581.24260.81911.536-0.3287-0.3869-0.38510.56550.3143-0.30060.25380.56050.00290.50390.1148-0.00760.57220.07350.564954.1117-43.123631.6694
81.9148-1.0780.40591.09640.84312.0821-0.33140.41930.2466-0.85380.2964-0.4183-0.0687-0.17730.00110.57150.0516-0.06450.48360.06560.470932.3599-15.6278-15.5505
90.26650.42520.46920.36520.36320.3923-0.2778-0.08790.28180.56250.69320.6336-1.1583-0.9241-0.00030.63250.18990.00190.51850.0390.551527.6714-12.4374-3.8506
100.01870.01790.04440.1137-0.03160.13290.2627-0.116-0.4205-0.257-0.19410.4132-0.3492-0.29420.00460.74930.1056-0.02090.7011-0.03170.638627.9005-22.140116.676
112.60.34410.02770.19530.6063.938-0.11460.02990.07540.24890.0577-0.0936-0.3261-0.151-0.00060.3251-0.01140.01740.3729-0.01740.301541.5754-29.51416.7979
121.4412-0.21070.52521.28030.55070.5331-0.07440.45370.087-0.1880.50210.3561-0.4317-1.3047-0.00020.57080.0532-0.09050.63340.09120.561724.7408-18.6597-13.6152
132.26-1.1135-0.33871.7915-1.36742.4668-0.01130.1766-0.1767-0.1797-0.07680.05070.0795-0.08060.00010.3621-0.0007-0.00420.3674-0.03890.336837.6915-31.2218-0.7342
140.29870.2948-0.11740.2383-0.12330.2526-0.16460.3588-0.0289-0.31440.01150.61290.2546-0.7990.00010.94680.1782-0.1180.9378-0.20351.368950.142214.58616.0134
150.08580.0666-0.02540.09470.05270.0653-0.2711-0.36870.32810.57770.29231.0764-0.1062-0.70920.00111.10790.10810.14840.9991-0.01591.610448.722911.472930.9628
160.4524-0.03890.48771.1943-0.95981.22380.2248-1.15610.49030.50350.0869-0.4296-0.94660.63850.00151.0185-0.0313-0.11360.6883-0.29110.985171.56615.49528.7305
170.0271-0.0309-0.01010.00370.02910.0079-0.01990.1059-0.2478-0.4558-0.17470.96840.3271-0.9992-0.00091.22520.0168-0.06950.9461-0.24641.901546.00537.6920.8766
180.62260.6450.23490.8170.1160.8441-0.0014-0.36090.12460.7661-0.00360.45630.2093-0.2290.00010.9192-0.0231-0.03460.6251-0.20180.899661.81659.4525.9726
190.050.03230.00440.04830.0170.0069-0.01720.0637-0.05980.20960.1947-0.03910.0708-0.1884-0.00061.08820.11880.07081.0225-0.47891.939648.024128.660927.6104
201.12240.26480.81211.2075-0.79991.3459-0.0339-0.26820.5372-0.18720.1635-0.4587-0.75770.4820.00030.9087-0.0046-0.08920.7026-0.1581.019970.014917.501517.8701
211.55291.2590.11241.0658-0.15643.2440.06520.0897-0.0069-0.1936-0.124-0.0175-0.1875-0.0538-0.00010.316-0.01230.01810.34910.02390.304741.4868-31.032218.8561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 7 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 25 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 60 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 65 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 28 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 29 through 73 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 120 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 35 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 36 through 60 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 61 through 65 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 73 through 106 )C0
12X-RAY DIFFRACTION12chain 'D' and (resid 5 through 28 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 29 through 102 )D0
14X-RAY DIFFRACTION14chain 'E' and (resid 5 through 25 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 26 through 61 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 78 through 105 )E0
17X-RAY DIFFRACTION17chain 'F' and (resid 10 through 28 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 29 through 67 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 68 through 73 )F0
20X-RAY DIFFRACTION20chain 'F' and (resid 74 through 102 )F0
21X-RAY DIFFRACTION21chain 'A' and (resid 75 through 106 )A0

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