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- PDB-7pq7: Crystal structure of Campylobacter jejuni DsbA1 -

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Basic information

Entry
Database: PDB / ID: 7pq7
TitleCrystal structure of Campylobacter jejuni DsbA1
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / periplasmic / disulfide bond / thioredoxin fold / posttranslational modification
Function / homologyThiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / isomerase activity / Thioredoxin-like superfamily / oxidoreductase activity / TRIETHYLENE GLYCOL / Thiol:disulfide interchange protein DsbA
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWilk, P. / Orlikowska, M. / Banas, A.M. / Bocian-Ostrzycka, K.M. / Jagusztyn-Krynicka, E.K.
Funding support Poland, 2items
OrganizationGrant numberCountry
Foundation for Polish ScienceFACILITY/2017-4/6 Poland
Polish National Science Centre2015/17/B/NZ1/00230 Poland
CitationJournal: Int J Mol Sci / Year: 2021
Title: Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis.
Authors: Banas, A.M. / Bocian-Ostrzycka, K.M. / Dunin-Horkawicz, S. / Ludwiczak, J. / Wilk, P. / Orlikowska, M. / Wyszynska, A. / Dabrowska, M. / Plichta, M. / Spodzieja, M. / Polanska, M.A. / ...Authors: Banas, A.M. / Bocian-Ostrzycka, K.M. / Dunin-Horkawicz, S. / Ludwiczak, J. / Wilk, P. / Orlikowska, M. / Wyszynska, A. / Dabrowska, M. / Plichta, M. / Spodzieja, M. / Polanska, M.A. / Malinowska, A. / Jagusztyn-Krynicka, E.K.
History
DepositionSep 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1374
Polymers46,7932
Non-polymers3442
Water6,900383
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7413
Polymers23,3961
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,3961
Polymers23,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.876, 51.726, 75.541
Angle α, β, γ (deg.)90.000, 125.143, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO(chain 'A' and (resid 5 through 15 or resid 17...AA5 - 145 - 14
12GLUGLULYSLYS(chain 'A' and (resid 5 through 15 or resid 17...AA17 - 2717 - 27
13HISHISARGARG(chain 'A' and (resid 5 through 15 or resid 17...AA30 - 4430 - 44
14ALAALAPROPRO(chain 'A' and (resid 5 through 15 or resid 17...AA46 - 4846 - 48
15PHEPHESERSER(chain 'A' and (resid 5 through 15 or resid 17...AA52 - 5852 - 58
16ASNASNLYSLYS(chain 'A' and (resid 5 through 15 or resid 17...AA61 - 6661 - 66
17ASNASNALAALA(chain 'A' and (resid 5 through 15 or resid 17...AA69 - 7569 - 75
18LYSLYSLYSLYS(chain 'A' and (resid 5 through 15 or resid 17...AA7878
19GLYGLYTYRTYR(chain 'A' and (resid 5 through 15 or resid 17...AA83 - 10083 - 100
110SERSERLEULEU(chain 'A' and (resid 5 through 15 or resid 17...AA103 - 106103 - 106
111PHEPHESERSER(chain 'A' and (resid 5 through 15 or resid 17...AA112 - 113112 - 113
112PHEPHEGLYGLY(chain 'A' and (resid 5 through 15 or resid 17...AA118 - 122118 - 122
113ALAALAASNASN(chain 'A' and (resid 5 through 15 or resid 17...AA125 - 127125 - 127
114LYSLYSVALVAL(chain 'A' and (resid 5 through 15 or resid 17...AA130 - 133130 - 133
115PHEPHELYSLYS(chain 'A' and (resid 5 through 15 or resid 17...AA136 - 141136 - 141
116GLUGLUASPASP(chain 'A' and (resid 5 through 15 or resid 17...AA144 - 182144 - 182
117ASPASPASNASN(chain 'A' and (resid 5 through 15 or resid 17...AA185 - 192185 - 192
21SERSERPROPRO(chain 'B' and (resid 5 through 15 or resid 17...BB5 - 145 - 14
22GLUGLULYSLYS(chain 'B' and (resid 5 through 15 or resid 17...BB17 - 2717 - 27
23HISHISARGARG(chain 'B' and (resid 5 through 15 or resid 17...BB30 - 4430 - 44
24ALAALAPROPRO(chain 'B' and (resid 5 through 15 or resid 17...BB46 - 4846 - 48
25PHEPHESERSER(chain 'B' and (resid 5 through 15 or resid 17...BB52 - 5852 - 58
26ASNASNLYSLYS(chain 'B' and (resid 5 through 15 or resid 17...BB61 - 6661 - 66
27ASNASNALAALA(chain 'B' and (resid 5 through 15 or resid 17...BB69 - 7569 - 75
28LYSLYSLYSLYS(chain 'B' and (resid 5 through 15 or resid 17...BB7878
29GLYGLYTYRTYR(chain 'B' and (resid 5 through 15 or resid 17...BB83 - 10083 - 100
210SERSERLEULEU(chain 'B' and (resid 5 through 15 or resid 17...BB103 - 106103 - 106
211PHEPHESERSER(chain 'B' and (resid 5 through 15 or resid 17...BB112 - 113112 - 113
212PHEPHEGLYGLY(chain 'B' and (resid 5 through 15 or resid 17...BB118 - 122118 - 122
213ALAALAASNASN(chain 'B' and (resid 5 through 15 or resid 17...BB125 - 127125 - 127
214LYSLYSVALVAL(chain 'B' and (resid 5 through 15 or resid 17...BB130 - 133130 - 133
215PHEPHELYSLYS(chain 'B' and (resid 5 through 15 or resid 17...BB136 - 141136 - 141
216GLUGLUASPASP(chain 'B' and (resid 5 through 15 or resid 17...BB144 - 182144 - 182
217ASPASPASNASN(chain 'B' and (resid 5 through 15 or resid 17...BB185 - 192185 - 192

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 23396.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: B5Y32_04750, B7Q70_04295, BCB47_05875, D4Q41_05880, DPG08_09245, DUY05_07510, DYE84_06245, EAX31_06480, F0166_06130, F0J04_04905, F6982_05945, F7521_05270, F7J47_05180, F8803_06690, F9778_ ...Gene: B5Y32_04750, B7Q70_04295, BCB47_05875, D4Q41_05880, DPG08_09245, DUY05_07510, DYE84_06245, EAX31_06480, F0166_06130, F0J04_04905, F6982_05945, F7521_05270, F7J47_05180, F8803_06690, F9778_05085, FVY60_01390, FW488_04080, FZ445_05615, FZ732_06740, G3M94_001567, GFF90_03350, GMG47_05310, GNO00_06010, GXA88_04885, GXS76_000973, GZ489_001237, GZ502_000952
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: A0A1J6PBD5
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: in Morpheus 2-33 conditions (0.08 M Carboxylic acids 0.1 M Buffer System 3 8.5 50 % v/v Precipitant Mix 1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2018
RadiationMonochromator: Double Crystal Manochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.55→45.83 Å / Num. obs: 55179 / % possible obs: 98.6 % / Redundancy: 3.52 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.043 / Net I/σ(I): 16.31
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 3.51 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 8791 / CC1/2: 0.772 / Rrim(I) all: 0.816 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXMRagephasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L9U

3l9u


Resolution: 1.55→42.65 Å / SU ML: 0.2354 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2002 2098 3.8 %
Rwork0.1768 53052 -
obs0.1777 55150 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.96 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 23 383 3476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01873274
X-RAY DIFFRACTIONf_angle_d1.61314432
X-RAY DIFFRACTIONf_chiral_restr0.0771469
X-RAY DIFFRACTIONf_plane_restr0.0119580
X-RAY DIFFRACTIONf_dihedral_angle_d6.32032740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.38081350.3583378X-RAY DIFFRACTION95.59
1.58-1.620.29941380.30623512X-RAY DIFFRACTION98.57
1.62-1.670.33251400.27133536X-RAY DIFFRACTION99.32
1.67-1.720.29561400.26353545X-RAY DIFFRACTION99.57
1.72-1.770.28571400.2423549X-RAY DIFFRACTION99.51
1.77-1.840.29041390.23173528X-RAY DIFFRACTION99.3
1.84-1.910.27231390.21223502X-RAY DIFFRACTION98.7
1.91-20.23431400.20753568X-RAY DIFFRACTION99.68
2-2.10.27861400.20993547X-RAY DIFFRACTION99.46
2.1-2.230.21781410.18143555X-RAY DIFFRACTION99.54
2.23-2.40.17191380.16643493X-RAY DIFFRACTION98.7
2.4-2.650.21141420.17463584X-RAY DIFFRACTION99.6
2.65-3.030.18531410.17193558X-RAY DIFFRACTION99.12
3.03-3.820.16641410.15273562X-RAY DIFFRACTION98.64
3.82-42.650.16891440.15043635X-RAY DIFFRACTION98.51
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)
10.46763992448-0.0804190043651-0.1550695201110.4532200836830.3411533917840.647936075389-0.3853704755990.276625163812-0.549935387161-0.6802115352560.0922022941814-0.5453383088230.2701666822710.00618042910244-0.0112237280790.363711193396-0.03718342586920.01717585708470.2416795448-0.0005046049223580.262881059044-6.4058730924132.13619176536.541594855
20.3498598874780.14714594154-0.5020446215060.341277882401-0.4586275091590.792257205321-0.0552763153012-0.3695915586390.1225125190310.169898198878-0.0520241138463-0.2553992369170.07390958910250.00336098459789-8.70596480765E-50.2774197120540.007988139724840.01445965356050.273887591612-0.05298346742340.278358130576-10.980504990243.367940179547.4748154545
30.4998862044190.5540610140350.1706289394581.329461113820.3808883481750.2289760809190.0453164788657-0.763591527834-0.4222168506340.364583644353-0.149052152554-0.2317907904130.006922081285460.202469321061-0.002428838994720.290978895852-0.0374080677426-0.02861139100650.4039449034630.08266686247450.266645728458-7.8203221468738.604452542756.2553264812
42.376020937312.01854375808-1.094958036953.16183054265-0.04110687304981.6918864080.0235780929196-0.429461931617-0.0887394634731-0.38163617208-0.00766062559384-0.177849052483-0.117540612694-0.0596984382924-0.09040280604940.2380507542-0.02491371746610.02159807719060.230307343913-0.01728360898530.249736524942-7.0167723941943.759588273145.1298694475
50.6450771752590.751224040232-0.8407198181331.12474338223-1.091554960811.416398202840.147435411252-0.0488196125844-0.183407800068-0.0274196706127-0.11404584926-0.00866622034088-0.03011928743620.2555589848520.0003112034433110.248155664008-0.034962246186-0.0212164447530.250436638778-0.06118786616240.25983702528-1.6781921529352.509812302643.8276165123
60.7232269162680.867359133266-0.412102510472.159307459410.08996156003391.453187727030.206260802706-0.609543418140.04385171357560.181396248201-0.21288584472-0.335809796424-0.1406193602370.287233583082-0.1574530101020.244179052323-0.066989762091-0.01771052546240.351887224588-0.03313372546430.231287883633-3.7533227578348.588208878254.0004469068
74.058905136382.83561838165-2.022662961642.25136666004-1.12828616531.31540961644-0.1441831198650.05001358646421.085386433430.309368117070.6247972880870.637532060767-0.387640324677-0.9208108277840.3024835766050.4127565083320.0149259750755-0.0004194903150050.517041066524-0.1777984609410.499689580767-18.247087684759.096456915155.2342343578
80.2167886038960.186741997037-0.1986140051590.348040612442-0.3639850061560.3525706402050.269078018443-0.3972816818650.3808062090830.22729384794-0.1614914764240.283146645105-0.3046435137130.202572618493-0.00105140632030.374751157033-0.03856280450020.04648959984680.305768767707-0.1619889228540.411335174722-6.7377293349561.452566617350.6075195142
90.360622204870.1746426358570.0438855018310.4240098261040.03307564969070.6772103361590.116678934709-0.3249358781160.383667892792-0.07711528888370.166066824454-0.437244510125-0.01419470667210.544021506593-0.0281446831950.305251904802-0.07247488755640.01114649660590.264363217589-0.08172921767530.3300354411142.1358501082660.905696703742.972951843
100.266970088466-0.1308436820780.3416161778941.18350077701-0.6244550063510.486995835957-0.1129021504750.2104198227460.296291189558-0.2732852349190.2132046109790.1373931169250.0845212595920.009347572850180.00181557809490.292612920717-0.0436923133272-0.007883644587820.232839904293-0.0605141882080.206184961509-8.3078006411844.849466039136.4170126971
111.4772774369-0.22534646150.88136787120.194203328902-0.1713034537640.669696401686-0.0742478583919-0.535068923646-0.416892354224-0.148345727640.06567813598490.09868538714130.389538179233-0.258808798845-0.03127636532740.296093428384-0.01804324015830.0467630313430.2447385607520.03295417241460.290589283805-11.496198836731.836451301345.1059871297
120.9654049311350.2095604479040.2528082158530.312946579525-0.3212475717720.5515939239640.118389047821-0.480897901099-0.830254389895-0.11488782996-0.0776909748992-0.04565702288310.197975401137-0.0958084247809-0.02041481581020.3498829687560.03239604446670.04694350959930.3231070748260.15747910240.469020307762-5.0383445063425.356503560948.1009985027
130.289273518708-0.05014721353650.3798477073490.518651913173-0.5875759721121.03086679505-0.214501266015-0.1296234210190.588411069876-0.3733464348-0.08946191124110.657841677377-0.267879544286-0.0478874232507-0.001189644513850.3244063844710.0121390953289-0.0405034000520.259263152958-0.0006832206807410.41987160291922.881771967931.95941236736.0528347059
141.513040168281.3311194823-0.1398073061512.35055872009-1.276043301831.480112964480.409152055654-0.8212585318860.3830030001120.219072053676-0.397784714470.260648504275-0.0214447950660.1013891413460.06695654390870.246851948515-0.06983890117560.02366985508920.431931365026-0.09819281864250.24674146966226.035126810524.580596547152.7321512851
151.508827127441.093753200111.249334975122.035935588460.2449805940441.371466602350.201332464806-0.4717678486870.229507889698-0.358057082317-0.02063438861720.2174101750590.07174911562170.04464468024920.04140169847390.248384435689-0.01176638460560.00464634373640.2483172187590.006394749285650.3606159913923.94127908521.135282636344.5451644351
160.6927070852420.5409370564260.881029967161.549021846230.7900029978281.128088639830.0521722791826-0.1811397363340.0194307700620.12635415713-0.1872785328550.2658162030.150220017581-0.2077845499270.0006297316827310.243022815443-0.02639599841320.01175111462830.2511326192610.005085274826780.22475534966819.182272629912.230011311343.5380869366
170.6887944405981.12391688698-0.4009914815951.89838689073-0.3871595553941.319873027360.244998553347-0.5213173411950.05748867404030.221038059901-0.34397256360.1606182207430.130644781442-0.10551226019-0.04720950589460.255351905723-0.07339145460480.005492492666770.448100243947-0.007690884087930.2111349154921.870653439615.958958660653.7522454381
185.47074511296-1.511305817671.201145123050.6136595942250.0805009636371.299176830090.198884583529-0.522063559972-1.306641131070.475987685049-0.279520144378-0.1532703330590.4486551807660.379419762637-0.5401036612980.376389579676-0.0160529491206-0.09951373557370.4866568507730.2109415501810.38376388217928.58033430243.6661888799551.3156012435
191.60827996064-0.5163058043720.7662539423111.577860696120.2072429410021.057849930750.0923340698197-0.0725315639101-0.0442679189698-0.133352036439-0.07721372133170.1487645542970.141309379344-0.0710259253557-3.14988763151E-60.265282773593-0.01479713067210.0004618236485150.2262070800610.03168139785750.18914720940821.04707085712.828517237138.6854733718
200.6916223121420.63277392521-0.3731172230711.78932714962-0.8986168536151.729844168630.123213757695-0.3046746496650.6043889055950.0945764389158-0.236257259127-0.0676011108005-0.1955265872160.228694671619-0.09680605528890.243563093173-0.0379798271867-0.04330299536480.242503124868-0.08548976040940.43305775965225.944288152935.706434694546.3958911099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 64 )
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 81 )
6X-RAY DIFFRACTION6chain 'A' and (resid 82 through 105 )
7X-RAY DIFFRACTION7chain 'A' and (resid 106 through 114 )
8X-RAY DIFFRACTION8chain 'A' and (resid 115 through 126 )
9X-RAY DIFFRACTION9chain 'A' and (resid 127 through 139 )
10X-RAY DIFFRACTION10chain 'A' and (resid 140 through 159 )
11X-RAY DIFFRACTION11chain 'A' and (resid 160 through 179 )
12X-RAY DIFFRACTION12chain 'A' and (resid 180 through 194 )
13X-RAY DIFFRACTION13chain 'B' and (resid 4 through 18 )
14X-RAY DIFFRACTION14chain 'B' and (resid 19 through 46 )
15X-RAY DIFFRACTION15chain 'B' and (resid 47 through 64 )
16X-RAY DIFFRACTION16chain 'B' and (resid 65 through 81 )
17X-RAY DIFFRACTION17chain 'B' and (resid 82 through 105 )
18X-RAY DIFFRACTION18chain 'B' and (resid 106 through 126 )
19X-RAY DIFFRACTION19chain 'B' and (resid 127 through 159 )
20X-RAY DIFFRACTION20chain 'B' and (resid 160 through 193 )

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