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- PDB-8ge0: Crystal structure of JADE1 PZP domain in complex with Histone H3 -

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Basic information

Entry
Database: PDB / ID: 8ge0
TitleCrystal structure of JADE1 PZP domain in complex with Histone H3
ComponentsHistone H3.1,Protein Jade-1
KeywordsTRANSCRIPTION / histone acetylation / transcription activation / Nucleosome / pVHL
Function / homology
Function and homology information


regulation of DNA biosynthetic process / negative regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / histone acetyltransferase complex / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex ...regulation of DNA biosynthetic process / negative regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / histone acetyltransferase complex / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / ciliary basal body / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / epigenetic regulation of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / regulation of cell growth / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of cell growth / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / nuclear speck / cadherin binding / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / centrosome / apoptotic process / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Jade-1, PHD finger / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. ...Jade-1, PHD finger / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Zinc finger, FYVE/PHD-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.1 / Protein Jade-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKlein, B.J. / Liu, J. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Guiding the HBO1 complex function through the JADE subunit.
Authors: Gaurav, N. / Kanai, A. / Lachance, C. / Cox, K.L. / Liu, J. / Grzybowski, A.T. / Saksouk, N. / Klein, B.J. / Komata, Y. / Asada, S. / Ruthenburg, A.J. / Poirier, M.G. / Cote, J. / Yokoyama, ...Authors: Gaurav, N. / Kanai, A. / Lachance, C. / Cox, K.L. / Liu, J. / Grzybowski, A.T. / Saksouk, N. / Klein, B.J. / Komata, Y. / Asada, S. / Ruthenburg, A.J. / Poirier, M.G. / Cote, J. / Yokoyama, A. / Kutateladze, T.G.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1,Protein Jade-1
B: Histone H3.1,Protein Jade-1
C: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,40618
Polymers62,4243
Non-polymers98115
Water1,856103
1
A: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1356
Polymers20,8081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1356
Polymers20,8081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone H3.1,Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1356
Polymers20,8081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.160, 78.160, 222.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 7 or resid 18...
d_2ens_1(chain "B" and (resid 1 through 7 or resid 18...
d_3ens_1(chain "C" and (resid 1 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAALAA1 - 7
d_12ens_1ASPASPA18
d_13ens_1ASPCYSA20 - 64
d_14ens_1THRPROA66 - 79
d_15ens_1LYSTHRA81 - 88
d_16ens_1SERTHRA90 - 92
d_17ens_1TRPGLUA94 - 112
d_18ens_1METALAA114 - 171
d_19ens_1GLUSERA175 - 187
d_21ens_1ALAALAG1 - 7
d_22ens_1ASPASPG18
d_23ens_1ASPCYSG20 - 64
d_24ens_1THRPROG66 - 79
d_25ens_1LYSTHRG81 - 88
d_26ens_1SERTHRG90 - 92
d_27ens_1TRPGLUG94 - 112
d_28ens_1METALAG114 - 171
d_29ens_1GLUSERG175 - 187
d_31ens_1ALAASPM1 - 8
d_32ens_1ASPCYSM10 - 54
d_33ens_1THRPROM56 - 69
d_34ens_1LYSTHRM71 - 78
d_35ens_1SERTHRM80 - 82
d_36ens_1TRPGLUM84 - 102
d_37ens_1METALAM104 - 161
d_38ens_1GLUSERM165 - 177

NCS oper:
IDCodeMatrixVector
1given(0.00486955961082, 0.999571889033, -0.028850061408), (0.500468832975, -0.0274133464642, -0.865320435247), (-0.865740858808, -0.0102248271222, -0.500388067704)-9.73762641617, 170.941620985, 170.312148506
2given(-0.023418126049, 0.99971280532, 0.00508903239865), (-0.494389613069, -0.00715629077345, -0.869210962881), (-0.868924911521, -0.0228712566504, 0.494415213922)-25.2984977113, 169.943432368, 67.2666576969

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Components

#1: Protein Histone H3.1,Protein Jade-1


Mass: 20808.127 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J, JADE1, KIAA1807, PHF17
Production host: Escherichia coli (E. coli) / References: UniProt: P68431, UniProt: Q6IE81
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.27819 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27819 Å / Relative weight: 1
ReflectionResolution: 2.4→49.51 Å / Num. obs: 28040 / % possible obs: 99.9 % / Redundancy: 39.8 % / Biso Wilson estimate: 46.4 Å2 / Rpim(I) all: 0.028 / Net I/σ(I): 28.2
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2849 / Rpim(I) all: 0.388

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.51 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2412 1371 4.9 %
Rwork0.2069 26582 -
obs0.2086 27953 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4180 0 15 103 4298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344267
X-RAY DIFFRACTIONf_angle_d0.6475759
X-RAY DIFFRACTIONf_chiral_restr0.0506641
X-RAY DIFFRACTIONf_plane_restr0.0052734
X-RAY DIFFRACTIONf_dihedral_angle_d13.45411586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.757586061735
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.558010914085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.3211260.2722571X-RAY DIFFRACTION99.15
2.49-2.590.31251320.24812603X-RAY DIFFRACTION100
2.59-2.70.29391360.23452621X-RAY DIFFRACTION99.93
2.7-2.850.29161500.24162581X-RAY DIFFRACTION100
2.85-3.020.33651190.25712657X-RAY DIFFRACTION100
3.02-3.260.27771550.22492629X-RAY DIFFRACTION99.96
3.26-3.580.25421280.21252646X-RAY DIFFRACTION99.96
3.59-4.10.22521330.192680X-RAY DIFFRACTION100
4.1-5.170.19081420.16982707X-RAY DIFFRACTION100
5.17-49.510.2071500.1972887X-RAY DIFFRACTION99.97
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)
10.5718197447420.08886241331260.02313589610830.3217308251880.1899279327970.359885526963-0.00244906204508-0.07085137939130.162765330633-0.1999688349450.181653250606-0.261472308758-0.3158370573160.2611228038921.93455134881E-50.418769234529-0.0630831141030.07548904536030.307216991642-0.03333135090030.26047145505452.610047934356.693347754789.7131035332
20.3176485232760.0569423105612-0.07645333704230.02335238067810.05344779470.251421497659-0.198054052023-0.01936593801410.168863652243-0.1032888518490.006344328330350.0604235697969-0.424060552284-0.0477970736944-0.0001815380459030.4536899036550.0208011708983-0.01119114745260.3040204598930.01305622011440.33207579932636.967295562357.832500670386.3850343373
30.6466577563130.04829164303850.4273756519620.783004955117-0.2561815065990.3800549316710.1879504852530.329618600113-0.107911825608-0.1963338541620.003825326867980.166279044479-0.438574232636-0.4370542181670.004631772530430.3596964842830.008445948115640.00474616175730.3092250998790.04364631391720.30193648610333.020938990349.506313806685.0923754042
41.031145208960.5044987572790.3703256614060.7844711889260.06648379073580.435238998370.113928434542-0.109843652436-0.5347342471450.00920143341112-0.310810685918-0.217485113794-0.03063857769080.263747008698-0.00148603631220.258290893254-0.0268363980186-0.004526710346320.3804361173670.0686213952420.34658775204837.555312263140.700213619594.4371598478
50.0420133383682-0.06596804773720.03521187829220.0918797095568-0.03280464732020.03535495841580.06208774529680.130406646465-0.090541149241-0.62223264807-0.6450828301830.444944736119-0.349664376841-0.128709700934-0.0003144608456970.5513691500740.145184041866-0.07828119868510.524645528632-0.05401033633610.51316863855525.716072809888.4951420864117.470107153
60.07195421908090.0319182259404-0.0007214089587960.0677994712162-0.03947604594570.03529529023430.152087908313-0.2516799498150.276348728301-0.0924803853671-0.3730480693860.01847804852360.166403622263-0.16789275268-0.0003849487256520.545759769744-0.000158371797640.0827291191510.376639412026-0.03735810417750.36353623312434.346382623779.0458999428116.692924036
70.0474659435811-0.065951141084-0.04066322867690.175363765728-0.04136880204660.1206660183290.1776708611450.08739389870560.216081414985-0.298440110089-0.2786453275880.197932271431-0.21337021003-0.128551191915-4.48875718106E-50.5879403073590.02116159915150.004185236859180.398399523992-0.005466102047840.34167936465634.818776074276.4452716678104.79959104
81.13746220295-1.502381325440.9911100757562.04458248915-1.37813308420.9446838905140.1972160909920.166140855022-0.505709650114-0.5358729632820.1403706385870.659037258866-0.185750107752-0.3613313303940.0607043907690.3904900155020.01841854536970.01660778801950.334832071245-0.05914848634120.25288136443934.855584772961.9203102315108.181526288
90.1081278667830.0181298156305-0.06994441762320.103044498559-0.05421175809130.05259255108870.142925282608-0.0385669610069-0.307686351333-0.1165845193170.0683621303530.140158077970.07182751338790.130447986772-0.0001746767294860.4363059820440.01910731825330.0448619706260.2780029880190.009046819357120.24601447903641.332805391563.4215702624107.978884461
100.436005753487-0.4660461903270.09526623061110.445870112324-0.1504235149170.281700137876-0.04765591285740.481000274458-0.148756608553-0.3812569029030.0642029690281-0.03275676833280.150740015888-0.1505624023940.00953270302930.3293586871080.01849936924570.07624411320250.2459849812870.01529833857820.24405819688642.694859879758.7612687879113.824836262
110.385183734365-0.126404397426-0.09069428824040.170730252692-0.1196210490440.4848110296490.177547697367-0.0798914856945-0.0100443137335-0.1001152573180.09929507548370.206692545263-0.116094819013-0.3830025027020.01715014099060.3496731878110.04503300590810.1186686353230.4022473497880.05058375168890.4098977599136.802814092660.5670898368125.109524934
120.282385177153-0.06137963710850.1257459469972.09226921069-0.461954978620.312575250454-0.0977977614926-0.1922529075580.0639451771831-0.1500124314030.0331869459544-0.820248698779-0.3074739853330.172250150259-0.03441827774280.437755073446-0.009460980135410.1305365358220.457208053416-0.02919492335780.40928925429241.212763211567.1404125497128.172725296
131.285527725290.885519623791-0.2380057047590.795386330306-0.4940574419370.63572195351-0.258434861806-0.3487471913230.8212160515160.4221662269520.051602625774-0.162414265978-0.431743100725-0.06457040207230.1231445071450.456477868140.010562047291-0.1077163645870.456683494127-0.166368719060.40327231350675.680295815979.89184641888.9861552191
140.161971860042-0.0364236561416-0.3129355559720.2311094782370.2929131649570.755989285886-0.3902893418340.1242438073650.09706382366340.214405190127-0.0694953910151-0.3237918779290.003944341193990.473030302929-0.08247637707550.405071074947-0.0342652865284-0.1536393223320.302224675803-0.02404056463980.56652911590666.391686782790.368715744983.9349090002
151.835680431521.22679869671-0.3575574905441.22854364343-0.3734033293170.447689678473-0.3402092003220.19350994041.061302377090.03222652091340.1119831908290.156233341846-0.260144211352-0.1556528089390.2703432409580.4090767994050.0951686428557-0.1735568702160.219027163596-0.1798539901810.64303378222151.780547726596.405038358180.3175565001
160.4845422743990.4224966591550.6054963570540.5517353273880.3057722339661.05600007081-0.052183410976-0.1675246247280.2363974480180.115846567345-0.1934444984880.2400382272160.212819929574-0.10817061515-0.07289354936380.281674369899-0.0366749835465-0.06020016155120.277292157525-0.03377159050450.41501417857444.243762027981.944190926676.4048002669
170.318132566671-0.02819766488190.2521761448410.2095169782180.1928233343970.41476521398-0.04448109146960.4130830490430.00165448926777-0.1540999542140.121848141535-0.5326060058030.5617028131520.4645110478890.007277040794340.482447998133-0.0210237798633-0.08842127385560.5271282563940.07426670413040.5102432419551.553168928977.914706747870.4913732425
180.2544639652030.2375536123750.2902614966460.2739441369590.3588341027030.4877620648610.00853330588207-0.1932595752460.02352692854740.247649587992-0.24069102959-0.00888151992674-0.0062440011016-0.0934852653151-0.9776751347650.394147929708-0.2469821351080.08930793554090.481237156979-0.1425888127030.29380248704859.850045725655.995881890297.7268792816
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 20 through 69 )CM20 - 6910 - 59
22chain 'C' and (resid 70 through 102 )CM70 - 10260 - 92
33chain 'C' and (resid 103 through 139 )CM103 - 13993 - 129
44chain 'C' and (resid 140 through 187 )CM140 - 187130 - 177
55chain 'A' and (resid 1 through 20 )AA1 - 201 - 20
66chain 'A' and (resid 21 through 39 )AA21 - 3921 - 39
77chain 'A' and (resid 40 through 73 )AA40 - 7340 - 73
88chain 'A' and (resid 74 through 87 )AA74 - 8774 - 87
99chain 'A' and (resid 88 through 102 )AA88 - 10288 - 102
1010chain 'A' and (resid 103 through 139 )AA103 - 139103 - 139
1111chain 'A' and (resid 140 through 170 )AA140 - 170140 - 170
1212chain 'A' and (resid 171 through 188 )AA171 - 188171 - 188
1313chain 'B' and (resid 1 through 20 )BG1 - 201 - 20
1414chain 'B' and (resid 21 through 64 )BG21 - 6421 - 64
1515chain 'B' and (resid 65 through 122 )BG65 - 12265 - 122
1616chain 'B' and (resid 123 through 171 )BG123 - 171123 - 171
1717chain 'B' and (resid 174 through 187 )BG174 - 187174 - 187
1818chain 'C' and (resid 1 through 19 )CM1 - 191 - 9

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