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- PDB-6uvk: OXA-48 bound by inhibitor CDD-97 -

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Basic information

Entry
Database: PDB / ID: 6uvk
TitleOXA-48 bound by inhibitor CDD-97
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / beta-lactamase / OXA-48 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-QHY / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTaylor, D.M. / Hu, L. / Prasad, B.V.V. / Sankaran, B. / Palzkill, T.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM120011 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries.
Authors: Taylor, D.M. / Anglin, J. / Park, S. / Ucisik, M.N. / Faver, J.C. / Simmons, N. / Jin, Z. / Palaniappan, M. / Nyshadham, P. / Li, F. / Campbell, J. / Hu, L. / Sankaran, B. / Prasad, B.V.V. / ...Authors: Taylor, D.M. / Anglin, J. / Park, S. / Ucisik, M.N. / Faver, J.C. / Simmons, N. / Jin, Z. / Palaniappan, M. / Nyshadham, P. / Li, F. / Campbell, J. / Hu, L. / Sankaran, B. / Prasad, B.V.V. / Huang, H. / Matzuk, M.M. / Palzkill, T.
History
DepositionNov 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,15314
Polymers113,1804
Non-polymers1,97310
Water7,368409
1
D: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5487
Polymers56,5902
Non-polymers9585
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
Buried area2460 Å2
ΔGint-16 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: Beta-lactamase
hetero molecules

B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6057
Polymers56,5902
Non-polymers1,0155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-y,x-y-1,z-1/31
Buried area2380 Å2
ΔGint-7 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.054, 123.054, 161.329
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase / OXA-48 Beta-lactamase


Mass: 28295.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The protein was expressed with a His-tag, which was cleaved off using a protease. The mature protein sequence begins with a Trp (W) (at position 25 in the endogenous enzyme numbering) ...Details: The protein was expressed with a His-tag, which was cleaved off using a protease. The mature protein sequence begins with a Trp (W) (at position 25 in the endogenous enzyme numbering) however protease cleavage left behind a GHM before the mature sequence.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, FNY87_29090, KPE71T_00045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 5 types, 419 molecules

#2: Chemical
ChemComp-QHY / 1-{4-[4-(2-ethoxyphenyl)piperazin-1-yl]-1,3,5-triazin-2-yl}piperidine-4-carboxylic acid


Mass: 412.485 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.77M Tris pH 8, 27% PEG550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationMonochromator: Double-crystal, Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.2→34.69 Å / Num. obs: 65748 / % possible obs: 93.77 % / Redundancy: 8.9 % / Biso Wilson estimate: 29.47 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.032 / Rrim(I) all: 0.096 / Net I/σ(I): 24.76
Reflection shellResolution: 2.2→2.278 Å / Rmerge(I) obs: 1.031 / Num. unique obs: 4164 / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR
Resolution: 2.2→34.69 Å / SU ML: 0.2203 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 3313 5.04 %
Rwork0.184 62411 -
obs0.1859 65724 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7907 0 137 409 8453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348246
X-RAY DIFFRACTIONf_angle_d0.715911158
X-RAY DIFFRACTIONf_chiral_restr0.05051160
X-RAY DIFFRACTIONf_plane_restr0.00331490
X-RAY DIFFRACTIONf_dihedral_angle_d26.49721182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.2832850.24461495X-RAY DIFFRACTION54.28
2.23-2.260.3478810.25861645X-RAY DIFFRACTION59.83
2.26-2.30.3011230.24242112X-RAY DIFFRACTION76.51
2.3-2.340.28811300.24662390X-RAY DIFFRACTION86.42
2.34-2.380.25161260.24242379X-RAY DIFFRACTION86.95
2.38-2.420.27511510.23082713X-RAY DIFFRACTION97.95
2.42-2.470.25531750.24352710X-RAY DIFFRACTION98.87
2.47-2.520.25441580.22692739X-RAY DIFFRACTION98.87
2.52-2.570.29341450.21492734X-RAY DIFFRACTION99.21
2.57-2.630.27311450.22042716X-RAY DIFFRACTION98.05
2.63-2.70.28691580.22452739X-RAY DIFFRACTION99.28
2.7-2.770.25481520.2072717X-RAY DIFFRACTION99.27
2.77-2.850.29491370.21082768X-RAY DIFFRACTION99.45
2.85-2.940.23661090.20822784X-RAY DIFFRACTION99.31
2.94-3.050.20991310.20122773X-RAY DIFFRACTION99.38
3.05-3.170.2441510.2082775X-RAY DIFFRACTION99.59
3.17-3.320.23351310.19862776X-RAY DIFFRACTION99.59
3.32-3.490.21981510.18632741X-RAY DIFFRACTION99.66
3.49-3.710.21471440.17042781X-RAY DIFFRACTION99.69
3.71-3.990.17911470.1572764X-RAY DIFFRACTION99.76
4-4.40.18641330.14512797X-RAY DIFFRACTION99.86
4.4-5.030.17461540.13592760X-RAY DIFFRACTION99.9
5.03-6.330.20651540.15952791X-RAY DIFFRACTION99.97
6.33-34.690.16791420.14552812X-RAY DIFFRACTION99.19
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)
18.00777483263-2.977384037331.745619114535.37418030357-0.9198002670422.221367737430.2452330492260.435512616708-1.51142374476-0.386931121471-0.07197395226360.09700674088250.8850839563280.0189157824279-0.1761765164781.20833041728-0.146710674470.1746569092110.396796392981-0.06608670644540.63281456213380.90144892611.08410994074-4.06407408785
20.9374016330750.7000282328430.07173273068191.49351409381-0.03660741219080.5384332731370.004768458152490.0650938113724-0.241732539132-0.1523827575010.0724200285775-0.1732190954770.107956421311-0.0374930446569-0.06565593935870.693756714647-0.2680071054850.09350202030580.269392970121-0.02387889062170.35794942036474.903553096910.34399378454.99783727736
31.733436308881.085142359820.2960719890772.071595008990.6910414228810.5566587921760.18416697298-0.3060390439990.009427400588850.807895718674-0.216004528121-0.2790159139910.127811697457-0.0120101795410.01394919065670.905379519736-0.354898181756-0.06365367167880.418436035090.02056133874920.34662959063785.893197528527.050966664319.3925531421
41.40341962930.762041809943-0.4813838976621.52726858677-1.005915799451.195490452370.166692379352-0.211400694010.05400126719090.320539689101-0.08107390143060.221197821834-0.0333476721225-0.100051944964-0.1160075691560.784639778711-0.315504070340.1830747244480.40440731369-0.05148964225030.36427612789671.300211524421.278953278921.8261451791
50.1766028133060.37723878233-0.02950273749170.801897830729-0.06588335635980.1769273591770.101129847148-0.104718025894-0.1076133828350.2201599982440.00683913538510.1474921334650.0830863008574-0.0780786600486-0.05584976272980.634269559338-0.3034631267520.1273676561860.296755460989-0.009859676198520.32507814703570.570557921217.732052290911.6449108726
62.78901876806-0.871584500020.3937970022384.82913155478-2.280266572282.1386264746-0.199171002121-0.25174500169-0.6032560005760.1166796502090.0410054313673-0.3691869169050.477382431302-0.1227811103370.1947167232550.651693742521-0.2321255253310.07264045471990.3135932052470.03003564708520.35867219760783.748592491115.45802334326.68639015997
72.71661740968-0.2837084476160.4332135992528.22322730287-1.875150118872.47569345469-0.1287662223280.0351156360902-0.268613198070.0759943803319-0.149268579332-0.7657540817280.3247181132430.1308225839450.2600392634030.615926584-0.1811454121920.1013931616240.216778776089-0.01269819071330.37071695970583.362775672511.7198525722-0.126538773946
84.313125776374.89491757762-2.449812282467.29672507724-1.881042818872.981384523030.138347341645-0.2977987057721.522257242710.465006200561-0.02671595238280.169278068986-0.9445298544560.00725824320911-0.09829496867211.202897727450.161058333944-0.2511574903070.415177317581-0.04915173003170.64918475089481.5483390937-0.793802381459.6407588847
90.910753076261-0.705944047569-0.07793188688531.616923424450.02738056531940.4955254075740.00665429456982-0.053514555990.2325453841730.1373957398030.0558816778463-0.178259848507-0.126586152696-0.0382639825784-0.05664839053420.6928534673640.274610361028-0.08279183955740.281719463249-0.02882047475150.34545416565374.8910460473-10.348596799950.6023425023
101.65660476563-1.21557482673-0.1430075066922.363462643060.6791112111230.603820446880.1909563185480.2866525037670.0858457977028-0.777608597983-0.21630717888-0.343706322701-0.149562896333-0.00768298551371-0.002086710868240.9359875864380.3591250076310.07678656952710.4271705583680.03816200792150.3369116722985.8740448976-27.063216764636.1950990065
111.33552718867-0.8417130220240.6719547484031.77570892335-0.9811672111341.004216242390.1614401056220.184331052399-0.0950691429065-0.308728532228-0.09075732042130.2268872605250.00757735495912-0.0927946411257-0.09385317006360.7790373171630.334248141682-0.1702119065140.411787475505-0.07159430561520.31844940816571.2594149998-21.241426189133.7502859986
120.183417752412-0.3775276635050.02135026434360.783294824461-0.04585471759420.1140561745810.09463614559980.09862264462980.115773465351-0.1969969148450.00361158620830.141286145884-0.0852263738902-0.0742761330939-0.05291858171110.6362127531380.307318770592-0.1210195867570.289396810688-0.01360824585410.31126795641970.5700258515-17.734724909843.9285837762
133.198937272280.434608185882-0.07595192474486.34192991985-3.580222954122.83156260208-0.1772927034850.2672604096780.554823107936-0.213674761044-0.0053834246953-0.425988634737-0.467225766297-0.1138704875340.2256038882080.6347967100570.228679548935-0.07501405825510.2898194708620.01411840260150.34779736166483.8020048194-15.519442329448.8831520615
143.62863513648-0.0702325360833-0.8122529807376.8049067112-0.5446882506642.03913372917-0.0744058898279-0.000721684395420.391205949542-0.0653733868095-0.0847485171101-0.549583513174-0.3394691717180.09173260639860.1389381754870.6063570405430.164017178929-0.1166392100190.204639385307-0.02091050677180.34418027858583.3695389284-11.732172728655.7325746945
151.17395210525-1.89117210107-0.4990717722064.925651465011.942499511050.9019039418470.04745817855130.03130915799830.4622687196420.1061753658850.05134374528380.568198781108-0.344269586581-0.011090545029-0.0993009955341.17509430041-0.0470656020932-0.2043122653240.322784000177-0.02833649311480.90641559903949.82427864997.00019579265.80101358775
161.185562577610.7779978058370.3138533518373.65019842822-0.4118496424180.902417966041-0.2178223078190.2081094543250.21643804457-0.4711822987910.124524852681-0.0144025063555-0.2546689540360.05788569420970.04620549429730.593308962457-0.2170673478320.02535837219070.230739252668-0.05968513854440.27677228432658.1722625926-5.146201050215.87914624275
176.6224034412-0.77392586456-2.521061271172.70425915504-0.1489167927542.770508443930.0224530823169-0.321370439404-0.3056602938440.2738314568570.12849852975-0.2595009285180.3372003634040.117741827747-0.156567524860.517146240091-0.121736097148-0.0003875793573480.188972189835-0.03613055580110.29912135395653.7923727828-26.031532667218.2530875743
185.99233430814-0.475500398524-4.434025680562.336875049470.4716004829728.67812691018-0.3321328085830.281043258734-0.616667279659-0.3893485239430.418434399979-0.7317746611840.4750736558160.628034529711-0.1073538234540.426387633659-0.0869276635480.068116955130.302556452118-0.2085025963930.45424682957868.1835016082-21.448315060313.175017685
190.6594869704330.7489947459270.4415764597611.292444467630.2778159969110.410444698217-0.1005829883610.172191986444-0.141951901185-0.1470980294230.166824066877-0.329910541445-0.09020875226150.202641073443-0.1360483177870.500275550639-0.2543661733040.1017435415980.293993641592-0.1218890287290.28447227749763.7030957515-14.54096650776.07337393641
203.168338389441.25633224641.922117343894.587144099062.159257045273.93858318547-0.3684654062480.01936299522570.541681401313-0.3096121226810.07097135877440.246979268904-0.3425305368450.06919596586990.3200265677920.444904446002-0.1498758444620.05393366730420.156035052183-0.05898228182690.25129173803850.4065783404-10.623835772810.4383977689
211.220708980730.5517758695080.3544265844613.17214425482.066179635741.81612075178-0.3063382343660.1069021003720.389750879947-0.4621376694410.03133223085970.455387360359-0.361249051579-0.08858983002780.287313309630.693123295644-0.141585710115-0.07788981530580.197783814553-0.03887420392620.35603789124648.177814571-4.58176948396.73554438683
222.00773723642-0.9018957585950.3981941107114.314274415260.1880025002950.506894485917-0.110857685594-0.105923566529-0.5765357141760.04176253657230.2108566894830.2667177664970.226225611330.0603071183241-0.1115936579740.9458415313160.2321096487450.1352791695690.3106599379020.02869975314450.53733005271451.938541506-3.7842267619452.4573301164
232.06360169159-1.067711488550.07375715059224.617365114571.115679200511.08067275668-0.03929601779650.06194228982090.25673299777-0.3186918400740.0121582562264-0.235343246827-0.1209618974030.0373383422640.0369336332150.4776056113130.118581638957-0.009366545856230.19588488905-0.07756995428370.24176075190456.899346026820.172031797640.3989704712
246.55980104410.1002670697355.3728247892.3000747575-1.01989899768.65625718771-0.337473451682-0.2252612054890.507725322320.3716775653010.444865166159-0.707872436-0.4400120313780.774886329355-0.1169812934460.4167115570450.100668959968-0.07561028461310.344011260573-0.2477043989690.47022379989868.195157671621.441422265342.4211422149
250.589635246721-0.717409254418-0.3984350052491.316956010740.2709504458060.374023431713-0.106250040205-0.1884998799710.1529708649080.1683661461790.181024821547-0.3183754827010.1061272398210.217178955405-0.1428541559870.4998231372840.255589119996-0.1101098404280.300776450778-0.1289835108510.2855843307363.710220792114.550193814449.5318724839
263.35515694134-0.802558698806-1.064372416314.779472302960.9980381844053.05051614908-0.368508499161-0.00722567066114-0.6083964163230.2554708528360.101245599830.2093758281920.3849964823890.1709991831980.3071562771120.4337588156050.148206314583-0.05957755243520.155584522535-0.06582266691530.27976481682250.40658297710.624600045845.1384681217
271.3326050459-0.657490503817-0.3625754902323.428388391292.054808065161.67530348451-0.306098834083-0.124908421397-0.388934993510.4707838036840.02701089306030.5281446477720.370104070067-0.08205934548030.2965317995320.6952805748090.1467849156180.0773188449660.20109873234-0.02427604070110.35227199995348.16185367284.583535519448.855440049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 218 )
7X-RAY DIFFRACTION7chain 'A' and (resid 219 through 265 )
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 119 )
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 142 )
12X-RAY DIFFRACTION12chain 'B' and (resid 143 through 194 )
13X-RAY DIFFRACTION13chain 'B' and (resid 195 through 218 )
14X-RAY DIFFRACTION14chain 'B' and (resid 219 through 265 )
15X-RAY DIFFRACTION15chain 'C' and (resid 24 through 38 )
16X-RAY DIFFRACTION16chain 'C' and (resid 39 through 82 )
17X-RAY DIFFRACTION17chain 'C' and (resid 83 through 119 )
18X-RAY DIFFRACTION18chain 'C' and (resid 120 through 142 )
19X-RAY DIFFRACTION19chain 'C' and (resid 143 through 194 )
20X-RAY DIFFRACTION20chain 'C' and (resid 195 through 218 )
21X-RAY DIFFRACTION21chain 'C' and (resid 219 through 265 )
22X-RAY DIFFRACTION22chain 'D' and (resid 24 through 58 )
23X-RAY DIFFRACTION23chain 'D' and (resid 59 through 119 )
24X-RAY DIFFRACTION24chain 'D' and (resid 120 through 142 )
25X-RAY DIFFRACTION25chain 'D' and (resid 143 through 194 )
26X-RAY DIFFRACTION26chain 'D' and (resid 195 through 218 )
27X-RAY DIFFRACTION27chain 'D' and (resid 219 through 265 )

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