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- PDB-7l32: Molybdopterin biosynthesis MoaE protein from Burkholderia ambifar... -

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Basic information

Entry
Database: PDB / ID: 7l32
TitleMolybdopterin biosynthesis MoaE protein from Burkholderia ambifaria MC40-6
ComponentsMPT synthase subunit 2
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / Molybdopterin biosynthesis / moaE / Burkholderia ambifaria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologymolybdopterin synthase / molybdopterin synthase activity / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Mo-molybdopterin cofactor biosynthetic process / cytosol / BROMIDE ION / Molybdopterin synthase catalytic subunit
Function and homology information
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Molybdopterin biosynthesis MoaE protein from Burkholderia ambifaria MC40-6
Authors: Sroge, C.D. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Oct 30, 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: MPT synthase subunit 2
B: MPT synthase subunit 2
C: MPT synthase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,91111
Polymers55,2723
Non-polymers6398
Water6,485360
1
A: MPT synthase subunit 2
hetero molecules

A: MPT synthase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3278
Polymers36,8482
Non-polymers4796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
B: MPT synthase subunit 2
C: MPT synthase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2477
Polymers36,8482
Non-polymers4005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.680, 93.290, 65.250
Angle α, β, γ (deg.)90.000, 90.103, 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
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 20 or resid 22...
d_2ens_1(chain "B" and (resid 2 through 20 or resid 22...
d_3ens_1(chain "C" and (resid 2 through 20 or resid 22...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALALEUA1 - 19
d_12ens_1ALAALAA21 - 30
d_13ens_1PHETHRA32 - 90
d_14ens_1ALATHRA92 - 120
d_15ens_1GLUGLUA125 - 144
d_21ens_1ALALEUB2 - 20
d_22ens_1ALAALAB22 - 31
d_23ens_1PHELEUB33 - 40
d_24ens_1ALATHRB43 - 93
d_25ens_1ALATHRB95 - 123
d_26ens_1GLUGLUB128 - 147
d_31ens_1ALALEUC1 - 19
d_32ens_1ALAALAC21 - 30
d_33ens_1PHETHRC32 - 90
d_34ens_1ALAGLUC92 - 140

NCS oper:
IDCodeMatrixVector
1given(-0.177746461837, -0.984042510317, 0.00815678816071), (0.984005818881, -0.177628409971, 0.0134423353564), (-0.0117789521172, 0.0104156545619, 0.999876377572)-21.6280278199, 30.9379761287, 5.82643920671
2given(0.187878131208, -0.982169722939, -0.00666656997871), (-0.982187585647, -0.18789402832, 0.00183867411661), (-0.00305849873607, 0.006202375615, -0.999976087775)-21.3467122905, 31.313905014, 71.0627614894

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Components

#1: Protein MPT synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / ...Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit / Molybdopterin-converting factor large subunit / Molybdopterin-converting factor subunit 2


Mass: 18423.844 Da / Num. of mol.: 3 / Fragment: BuamA.00098.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria)
Strain: MC40-6 / Gene: BamMC406_1760 / Plasmid: BuamA.00098.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1YRH1, molybdopterin synthase
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen, B5:10% w/v PEG 20 000, 20% v/v PEG MME 550 0.03 M of each sodium fluoride, sodium bromide, sodium iodide 0.1 M MOPS/HEPES-Na pH 7.5: BuamA.00098.a.B1. ...Details: Molecular Dimensions Morpheus screen, B5:10% w/v PEG 20 000, 20% v/v PEG MME 550 0.03 M of each sodium fluoride, sodium bromide, sodium iodide 0.1 M MOPS/HEPES-Na pH 7.5: BuamA.00098.a.B1.PS37913 at 49.6 mg/ml + 0.5% n-Octyl-??-D-glucopyranoside: cryo: direct: tray 317329b5, puck xxu3-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52076 / % possible obs: 98.8 % / Redundancy: 3.672 % / Biso Wilson estimate: 37.499 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.056 / Χ2: 0.939 / Net I/σ(I): 16.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.952.9910.3923.0433720.9150.47487.4
1.95-23.3310.3723.6537400.9320.44298.5
2-2.063.7450.2725.4336600.9570.31999.9
2.06-2.123.7810.226.4636180.970.257100
2.12-2.193.7820.1648.334600.9830.191100
2.19-2.273.7750.12910.2533730.9870.15199.8
2.27-2.363.7920.10711.9131870.990.12599.7
2.36-2.453.7910.09213.3231390.9930.10799.9
2.45-2.563.7830.07216.3729560.9940.08499.8
2.56-2.693.7780.06118.4928760.9960.07199.9
2.69-2.833.7980.05320.8827090.9970.06299.8
2.83-33.7820.04724.0625720.9960.05499.9
3-3.213.7560.04326.4724270.9970.05199.8
3.21-3.473.730.0429.3322740.9970.04799.8
3.47-3.83.7270.03631.3620730.9980.04299.8
3.8-4.253.7120.03432.5718720.9970.0499.5
4.25-4.913.660.03333.5816500.9980.03999.8
4.91-6.013.60.03432.8714100.9980.03999.5
6.01-8.53.6040.03133.710940.9980.03699.5
8.5-503.3930.0333.776140.9980.03597.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19RC4-4035refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2qie as per Morda
Resolution: 1.9→48.25 Å / SU ML: 0.2188 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1986 3.82 %0
Rwork0.1792 50069 --
obs0.1801 52055 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 8 362 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793380
X-RAY DIFFRACTIONf_angle_d0.84724601
X-RAY DIFFRACTIONf_chiral_restr0.0607523
X-RAY DIFFRACTIONf_plane_restr0.0083598
X-RAY DIFFRACTIONf_dihedral_angle_d12.32281206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.560993342605
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.24405046506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.31761320.2643114X-RAY DIFFRACTION87.21
1.95-20.25681250.23983577X-RAY DIFFRACTION98.01
2-2.060.25121620.20853541X-RAY DIFFRACTION99.87
2.06-2.130.23941420.19153656X-RAY DIFFRACTION99.95
2.13-2.20.21481550.18143592X-RAY DIFFRACTION99.95
2.2-2.290.1821330.1733583X-RAY DIFFRACTION99.79
2.29-2.390.20041440.18173622X-RAY DIFFRACTION99.68
2.39-2.520.23571710.17983581X-RAY DIFFRACTION99.84
2.52-2.680.20911360.18073610X-RAY DIFFRACTION99.89
2.68-2.880.21421480.18713601X-RAY DIFFRACTION99.84
2.88-3.170.20651380.18793628X-RAY DIFFRACTION99.81
3.17-3.630.18931280.17583670X-RAY DIFFRACTION99.82
3.63-4.580.19311280.15523614X-RAY DIFFRACTION99.6
4.58-48.250.17781440.17513680X-RAY DIFFRACTION99.3
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)
14.580867199330.1350247007582.982240492875.773612878232.050888689628.595818527550.07526080855150.2073657661740.5718808635580.1093788650140.1125371981680.36429816461-1.38449968581-0.304879985873-0.1995226673580.4085486683910.03594518963620.03022735662480.2031310792850.08081495647640.27031212632-4.1108833407224.323229180619.5843706653
23.786717137380.4948000824710.2365984549851.86807267763-0.8655836042294.062471137440.0151794090306-0.3551246342030.4599022179460.09144640479390.1120570768790.117485558916-0.591299414899-0.104490153345-0.07629741560070.2837306334520.08918350936940.02525240343510.231449906832-0.06195773754720.279289045757-10.819848994221.859186720532.8659347451
32.947305708320.4607266693790.6434642982371.43686711759-0.4421252710794.043461022-0.01326227194160.5951850651440.185349553095-0.261102168127-0.0169137593491-0.293239182483-0.4286125610380.8340768188690.04633752514860.246485878818-0.02530757018880.04017177965460.3308005520640.03563346943390.2918957013793.8539677107817.947201457218.3961119258
44.51858225413.43431301175-2.447889548656.50045344708-4.229516394217.25545156311-0.1548592723680.6226484382580.194845003185-0.535478334520.3198914327750.274393404721-0.00528936656361-0.413071021672-0.1963102583030.1704582301180.000827713924971-0.02797067969550.2557851131890.006119262715380.199321985242-10.8133778319.5120194313317.4625647149
53.055796339651.37402972467-0.2812036109492.80985124289-1.408972348164.35808249071-0.01305547494270.114635297110.1552597275850.0284799016768-0.05457085911270.0181337451836-0.504663860690.2359151434610.002111595105720.1798123448690.0191100778921-0.003709873737430.1417415997930.001144455384810.177318955335-2.284168685217.512453178724.0396860196
63.045379095971.47425350814-1.81479039712.45351602535-2.270637979342.45850118807-0.1160325967730.225084525415-0.120378827061-0.2841749151150.0379308642139-0.08964654450290.19987231571-0.1570218281290.0493289917090.1418489702260.00360452033401-0.0055625185430.156404475208-0.01405936222720.224234060523-3.305950760197.6648390731825.6770540936
76.365501080572.50402624385-5.425150085054.49300347603-1.973683434647.1569826512-0.164818135580.05197060361860.113791308922-0.02827104390090.0777344463274-0.6593505367640.09527183649331.842592033570.3545971519260.295696775091-0.08980185798440.003835155728920.7456040559380.03688640141370.2764661102225.9556779217414.78824345637.48532408314
84.04648232527-0.263272084448-1.167834627712.63043005255-1.760725032032.29204575786-0.2541013225420.739199633297-0.574865314988-0.338170130948-0.316533181531-0.7852640688750.3376863228471.18270336170.5663849572810.4767083618660.0219104205520.07766404424110.858919945495-0.0415254832860.3750714310698.7510615916211.36175541375.49408244233
95.128883073091.97252505801-4.743777083079.70478561101-6.530187925838.05599024899-0.5323616116481.5691888291-0.451902245751-1.00507802199-0.193357618068-0.5961544453470.8825082715070.5957693618870.5605533522350.2702499595140.02332482778690.007657569350250.35158405232-0.03024025498530.418893285526-1.07893621118-2.3121630365222.2244633194
103.46853506079-0.5842808105450.8001558321434.33606744977-1.818851528077.924684638840.04924378312070.0193418795706-0.602629311096-0.03855217835380.1522936084030.6829929910760.355691174091-0.601263152091-0.1475773777770.234735133204-0.0103235281578-0.02390093673190.272832266636-0.03391247126930.481457507677-43.945068594121.178804079830.7031462859
112.95216418493-0.2007104679750.2124778324285.81326502427-1.67023486285.88265251581-0.157614025932-0.0983266288575-0.5213623802840.136430226690.0971855205680.2456322986890.670061252315-0.121356210763-0.07429611365860.2658065081780.07538040017460.05442460021940.2356494698150.01851180728910.321805658355-37.163142695721.016962441238.2448534703
120.5744969517010.9122814715871.079124861896.89846063221.064359890162.750968450050.0233745396639-0.3437983440660.1836887639512.11997200798-0.508190698901-0.7500559426590.1374351244010.2590937343910.3946984633970.9197898316190.155727854667-0.04665994641080.607260086850.05733136195980.895390820387-43.233478698443.603837511124.2506364887
134.42544052813-0.601972486602-2.677341219464.965228479723.461692108933.6592060221.000784183731.21030302589-0.122912847661-1.3301794489-0.8878338111761.094875726710.229569369015-0.4855416548940.3493711019330.6826321351270.235149469631-0.1624303453960.516472117724-0.1181897278260.340996283668-40.320969197428.516386367914.141865218
144.8223044163-3.064670324892.274045014363.62232501284-0.9832649786684.455740934410.6155468383870.45142887774-0.626055389838-0.746052849673-0.3035385895070.3549545285120.7898078336440.118387753105-0.07753838842830.3301424238520.196671568124-0.03479138934320.32399947067-0.07578867191280.250885959742-28.606039544518.904625278924.2563865905
154.12470401424-2.240556304920.9778847100583.92498871256-0.3974418380223.80483531419-0.149172648153-0.147353892254-0.1880343470680.04967299921890.1186104885590.286577745703-0.108613168002-0.435359381044-0.03945224321580.2072320977380.06226206077750.01580451445540.180193560212-0.03435588930640.248964606762-38.274695900425.851339585230.0962403368
164.02567176131-2.850582728412.748401125293.40182179389-1.577477147938.178988806730.1217887014730.7140369446850.271826041441-0.656230463747-0.394486217726-0.261535763484-0.3977324006260.6031667827360.1903399555320.3570672113510.09110669965890.02453584419570.3224727694380.02538392258380.237178452105-32.65723795231.506497560421.3380207431
177.21772408255-1.890447502255.043031515161.50388265286-1.912587474593.791391745030.05294784258620.6599168150621.9646027616-0.579633820153-0.265490804463-0.58958538564-0.607951053350.2151713710040.3447815966090.5410347929530.05541048132820.119239146330.5213223690230.0474300258960.695961324801-22.175990297231.551138552225.0553189897
182.932191528860.318360746071.466446019474.023404998531.132228874948.45740839448-0.171331707759-0.4586928406140.1105523719970.4150615957150.2999065988860.576523011982-0.426799516302-1.09291843587-0.1287094877810.4077421227420.1692354115380.1590790134090.4563506296520.09696979981960.345422179914-46.110040848330.828118164251.8065870678
191.60098257255-1.513533600170.1307619473714.7778995498-0.817983217511.366021541550.0229015684246-0.0713705908775-0.131845333192-0.304283113022-0.03741759746770.2179482035820.3021232710850.0701811101252-0.007769830691670.2134887544610.0464634058714-0.01861034838040.2350478495920.01549728679270.267408408203-42.745132007934.910825953439.4618719787
202.01491004545-0.439272984856-0.6335609687653.26515251541-0.05590767032935.41834634978-0.295002407028-0.759268623421-0.1535862760541.191138752330.3600979422470.1541194941110.1323771158230.144373940603-0.03895739928560.4346505288580.2615469117080.005341793417310.5190935058770.0321824130260.309541679186-35.537614854331.571741153555.9444052794
211.74682738466-0.458277647817-0.06995917186564.34883434231-0.3903115245523.67093759133-0.293865174532-0.347897424618-0.123597292170.4067425662940.2698894902720.2216460177920.475708085996-0.0724911763801-0.0247110927440.2934498777250.1493752968440.0465907025820.2696874652140.03421768235080.222675688897-39.141245679830.216103959147.1580143119
221.44271551231-0.548093544564-0.3301857060463.46648760627-1.955574747496.4674710824-0.189697639807-0.526795786442-0.1295903241720.7274437952940.236825452174-0.2757005566980.4415555636030.9577107452210.2508300189840.3666220787170.197187888147-0.04921248469930.422365639934-0.02166971215410.288324558085-30.790966422631.091941977749.9174749364
235.03064110779-1.491103373850.9994282358085.02110083906-1.880410793667.87028231793-0.0120802014139-0.379314545042-0.170909239991.092471586450.227436421709-1.067061259130.08482810052580.905463598192-0.09792205338681.008135750160.500125196272-0.05160736473170.7558769903620.0401742206260.522419445598-28.719893972823.293691328962.1360359017
245.883779663840.0863704169869-1.846027076823.60804346496-0.5841675978416.68217253935-0.151443726714-0.290395072637-0.7593399124520.568524555232-0.450732947155-0.6067380423550.126076885920.8360241262890.03593952313150.3030740617540.111151610682-0.03048781292990.62589747197-0.1385299071890.882222087813-20.502185839336.08916848347.2711748405
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 12 )AA2 - 121 - 11
22chain 'A' and (resid 13 through 28 )AA13 - 2812 - 27
33chain 'A' and (resid 29 through 56 )AA29 - 5628 - 48
44chain 'A' and (resid 57 through 72 )AA57 - 7249 - 64
55chain 'A' and (resid 73 through 102 )AA73 - 10265 - 94
66chain 'A' and (resid 103 through 120 )AA103 - 12095 - 112
77chain 'A' and (resid 121 through 128 )AA121 - 128113 - 120
88chain 'A' and (resid 129 through 142 )AA129 - 142121 - 134
99chain 'A' and (resid 143 through 152 )AA143 - 152135 - 144
1010chain 'B' and (resid 1 through 22 )BB1 - 221 - 22
1111chain 'B' and (resid 23 through 36 )BB23 - 3623 - 36
1212chain 'B' and (resid 37 through 48 )BB37 - 4837 - 43
1313chain 'B' and (resid 49 through 56 )BB49 - 5644 - 51
1414chain 'B' and (resid 57 through 72 )BB57 - 7252 - 67
1515chain 'B' and (resid 73 through 102 )BB73 - 10268 - 97
1616chain 'B' and (resid 103 through 137 )BB103 - 13798 - 132
1717chain 'B' and (resid 138 through 152 )BB138 - 152133 - 147
1818chain 'C' and (resid 2 through 12 )CC2 - 121 - 11
1919chain 'C' and (resid 13 through 36 )CC13 - 3612 - 35
2020chain 'C' and (resid 37 through 72 )CC37 - 7236 - 64
2121chain 'C' and (resid 73 through 102 )CC73 - 10265 - 94
2222chain 'C' and (resid 103 through 127 )CC103 - 12795 - 119
2323chain 'C' and (resid 128 through 144 )CC128 - 144120 - 132
2424chain 'C' and (resid 145 through 152 )CC145 - 152133 - 140

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