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- PDB-6pua: The 2.0 A Crystal Structure of the Type B Chloramphenicol Acetylt... -

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Basic information

Entry
Database: PDB / ID: 6pua
TitleThe 2.0 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / left-handed beta helix / hexapeptide repeats / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase / acyltransferase activity / response to antibiotic
Similarity search - Function
: / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, Y. / Maltseva, N. / Stam, J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Citation
Journal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
#1: Journal: Protein Sci. / Year: 2020
Title: Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species.
Authors: Alcala, A. / Ramirez, G. / Solis, A. / Kim, Y. / Tan, K. / Luna, O. / Nguyen, K. / Vazquez, D. / Ward, M. / Zhou, M. / Mulligan, R. / Maltseva, N. / Kuhn, M.L.
History
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Oct 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 1.5Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / 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: Chloramphenicol acetyltransferase
B: Chloramphenicol acetyltransferase
C: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,35425
Polymers71,5373
Non-polymers1,81722
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16000 Å2
ΔGint-145 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.058, 100.058, 128.036
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Chloramphenicol acetyltransferase


Mass: 23845.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0300 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q9KMN1

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Non-polymers , 5 types, 378 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50 % v/v (+/-) 2-methyl-2,4-pentanedio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2→39.42 Å / Num. obs: 50618 / % possible obs: 99 % / Redundancy: 7.6 % / Biso Wilson estimate: 37.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.025 / Net I/σ(I): 37.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 50618 / CC1/2: 0.746 / Rpim(I) all: 0.415 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EEV

3eev


Resolution: 2→39.42 Å / SU ML: 0.1869 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4457
RfactorNum. reflection% reflection
Rfree0.1882 2356 4.67 %
Rwork0.1628 --
obs0.164 50415 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.3 Å2
Refinement stepCycle: LAST / Resolution: 2→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 50 356 5430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725255
X-RAY DIFFRACTIONf_angle_d0.76947124
X-RAY DIFFRACTIONf_chiral_restr0.0591722
X-RAY DIFFRACTIONf_plane_restr0.0048911
X-RAY DIFFRACTIONf_dihedral_angle_d16.34292987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.26081430.23522776X-RAY DIFFRACTION98.61
2.04-2.080.23481360.22362820X-RAY DIFFRACTION99.86
2.08-2.130.23551120.20632815X-RAY DIFFRACTION99.83
2.13-2.190.25221440.20032747X-RAY DIFFRACTION99.69
2.19-2.250.22571330.19332827X-RAY DIFFRACTION99.73
2.25-2.310.23491280.19082804X-RAY DIFFRACTION99.66
2.31-2.390.21751420.18422787X-RAY DIFFRACTION99.49
2.39-2.470.24511680.18322787X-RAY DIFFRACTION99.73
2.47-2.570.26741160.19962834X-RAY DIFFRACTION99.56
2.57-2.690.24181420.1872785X-RAY DIFFRACTION99.42
2.69-2.830.22841490.18782806X-RAY DIFFRACTION99.26
2.83-3.010.22961400.18042824X-RAY DIFFRACTION99.53
3.01-3.240.19771410.17632834X-RAY DIFFRACTION99.47
3.24-3.560.19231360.15482843X-RAY DIFFRACTION99.67
3.56-4.080.14371360.13172868X-RAY DIFFRACTION99.67
4.08-5.140.11591300.11922906X-RAY DIFFRACTION99.67
5.14-39.420.17951600.1622996X-RAY DIFFRACTION99.31
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)
18.182154943275.083795779993.088714595276.59388757007-0.3673335717952.69759737355-0.4215256809981.178055634540.470672102944-0.9180991853190.363919608604-0.07165725596710.0728775510990.123825497202-0.007024613552660.6195295331-0.0287164532198-0.06021099786870.5751016969620.0972139413740.27940066293932.5319584374-28.3697130542-15.3756199529
21.898200460721.631863388120.48443436223.971893710710.5455400144431.95287477657-0.1649501075320.3023053040660.0403212551415-0.4297299553860.1173248647360.422973581365-0.183004026271-0.2415104858390.05866231267020.4065232349310.0179251662204-0.03732845594690.488801246463-0.01247578158790.2951280647723.0000575703-36.1169330429-8.72168536181
30.917199081918-0.278778192344-0.07501258081032.58896215242-0.3654716601340.560898149206-0.05256013934330.210892455028-0.277136865412-0.3126603569970.0470238907633-0.004017687655220.0617391734399-0.0511357837732-0.01166022766890.355326256476-0.0181872289970.01548970284880.406554738913-0.03299009372480.32491010467531.5480747281-47.0408067195-4.53638909287
48.48671097201-5.28818255195-1.677058421753.522221529031.785581808463.620068922610.4591432660960.678550833863-0.834414357197-0.41272362607-0.190301021270.03539821557540.200833467217-0.0851375619426-0.1760074286230.479614862034-0.0388934991953-0.02149653843340.397621657221-0.06901998147470.61437108741734.6386785859-65.3812870305-4.81424327777
52.0275637316-0.444940249506-0.7750602113970.9006883277430.4104075778190.739371658768-0.0865934371169-0.0208815684235-0.1179560411050.07808118494530.04764954847620.01304461147210.01866782687690.05511487369770.02146653077840.3265235852160.02887429577990.02537360100280.3585683112860.03067886247930.25274424369631.2820862328-37.05197517035.98849150494
62.82140290814-0.256224784285-1.355189075741.16778836221.032086969761.34405722867-0.0518875475104-0.07577162088490.2109084077170.142979580476-0.002348855065230.06662858139590.04160959580460.1897263409940.04242896146550.3368939887170.02732375711610.03419334352640.3466630016560.062427445540.24334935838524.4407520841-29.351293602415.7664316736
77.223644918491.597089947312.829439425511.43311415080.00276762029434.18962517622-0.1429360149540.3523376835520.722954367033-0.255265675577-0.137576151180.258493313049-0.254663483238-0.1669171142510.2650591123340.3568160018920.04446234306220.01433077902110.3589003567140.03943001729520.35042062951613.8697124633-21.3159621394.26651484801
84.605052407431.519661411586.264342989079.406404889172.24056252538.67766559088-0.0968683490857-0.3188305889020.269533584382-0.288630387207-0.1939205368450.457525960813-0.211159784046-0.8173120650460.2697364354240.3240668151160.04125328961230.01670667942250.312712252865-0.007887724530620.2968941958458.42340624756-21.596557073814.1597075142
94.60892775941-0.705967028646-1.575088124599.82416892390.3779484510961.929302044030.07781221426221.12138121782-0.877092263013-1.00844097678-0.0872331542243-0.7858717717380.0333751155785-0.270129065220.2962722686360.6360394846060.0003905163953950.2162962063110.680046685732-0.04564745801150.39165019641356.1471516414-33.0433065335-18.1520094162
103.14604200302-0.574368472995-0.2298589094474.29705009732-0.136636393241.6006657092-0.006134496322780.769508469190.389056211511-0.603172967579-0.170196268213-0.428116791373-0.2002953758530.2639573581110.1346309873820.483416462319-0.05457275840280.04752551024320.5087732683660.1286765128280.35709074787255.4508808558-20.7571852519-11.9172936624
114.087667747810.355541329366-0.6701942696333.09693253221.667390916643.00094444908-0.0882627556490.5306137341640.527376566049-0.5967704215990.04730913940360.086380082418-0.298045919465-0.1818997895940.06312602509230.409356596965-0.0324964150169-0.02401909692810.4261663173560.07992905760470.28921305872545.0057998205-22.3554750779-10.0466530993
121.90838360150.0719335687186-0.6405540854970.313136490776-0.3600300736250.6118310030550.00376682446033-0.0903077002795-0.01181380396540.02063529184720.0391866638373-0.0194784827193-0.038181092045-0.0487938081829-0.006776366072520.346172235044-0.00218359192688-0.002230582271760.3561137882510.01058262826950.28063312775841.0433903135-22.6587424797-0.688874923318
137.994490178121.68592564776-1.163246496643.11944812078-0.5833681395481.80888062348-0.2070510219610.8061229851650.896448799371-0.2245425569830.2859111142810.496545387389-0.210230440844-0.545037825649-0.1708099761050.5024945777270.06981820885010.001073463461460.4974793782460.08928436974330.34219592159825.8512996313-16.5047873543-2.5639531716
142.184689497240.590152581869-0.1628192036783.55248508423-0.4306051888581.16912274458-0.0255442748421-0.1217152723790.04104413301290.117184596933-0.0302134168923-0.214242163681-0.04560785944930.0328220704850.05795434297580.331130833215-0.0138360842486-0.007883831816890.348714192130.01966598350560.30387389763354.3011968558-25.14163658731.26704265507
152.950848955941.759251670960.1864963528044.59336434926-0.3951100095480.438531253749-0.0286269799459-0.268298305161-0.05520694700350.4847280594050.129118505465-0.314143752479-0.1250755471750.28077316550.03999663646280.334229486155-0.0164797790899-0.02013786441790.351767952480.01003870235010.2193860934850.2599246584-28.79698926385.94706541002
163.239064938481.187694355630.1011620415223.48678688871-0.2090604881051.4422618127-0.0592563686012-0.67323747013-0.2287293863590.462926636832-0.182039234042-0.626526800984-0.109242333169-0.01617692106380.0880029611140.388226856395-0.0175612317915-0.0897149668750.4461039169890.03580562249040.36657964388158.4818175836-29.442409354110.3179588746
172.003535132340.766094770897-1.476626621813.54252497954-2.60262775798.217228029810.11193184868-0.354235587779-0.1391184260690.607693021788-0.387972116153-0.742990799175-0.3754017480670.4928351648480.2217126714890.384215149116-0.0595405812404-0.1450627734430.4687008443990.06001315512890.52562457719570.2555781641-17.30329839455.39765767589
185.31260269974-0.214200725322-0.1283190000129.49540032747-5.409532905835.64150418767-0.321456891253-0.078103781235-0.93813835457-0.268179368632-0.330632954622-2.080137889280.2767328841940.0274614159990.6553304983790.3710197444-0.0532932274334-0.01590380376750.4571072195120.06973075257970.82712020702677.2904734261-21.5326565142-3.56349419701
194.893422489694.04807498828-1.174809094739.56274064707-0.08400476256662.487594461340.346407526738-0.609540081043-0.2994602655360.9118624095-0.499790017494-1.15065542154-0.2861354573760.327083373440.5186554704010.476869936964-0.0779151790741-0.2610014327720.5564523140510.1546022393070.84689095332479.1741598809-14.26213515976.23485960901
209.14614489228-3.00310631702-2.355154421891.828127743932.336619587163.82488485960.5115730785550.884949844415-0.224683745813-0.172599923383-0.499822234570.3187315661230.0879975795095-0.1081374982630.04377803597940.544883210509-0.05553378726270.1238727221710.665086659621-0.1947135505390.51829440656339.896645221-51.4165835403-16.9765335603
213.7281248571-0.23067481997-0.06525308627463.272618194130.1569000452382.15220656684-0.1308183144330.63041806006-0.301156440405-0.5239858782430.0993703344913-0.6024817224030.2073210294060.1303022654480.0674556788680.475903498033-0.005142865600010.1503676206880.436351700108-0.08365708144320.46442881788254.9476133754-51.1068952183-12.4288964096
221.897578938610.622803389573-0.01468507390742.685825471330.07781965479430.442911978142-0.07876604954990.158662279844-0.343348919851-0.1040290698070.0214870176251-0.603413248821-0.0241043177450.0529803293280.03935990740360.339829048881-4.49576739368E-50.06688400681680.3736453964640.0108326954110.46530239130359.8748193827-42.7100716603-3.52811568204
234.3960596933.8464794905-1.685077793133.62896591981-2.067687072181.95853425189-0.2121319252660.167885458771-0.16488497783-0.694489982662-0.0465733632455-1.28211149373-0.03761277237870.1393819714630.2789809570590.4829117862190.01632534153560.1612160475490.505553915074-0.008945562501530.66036971190671.816446289-32.7806554502-8.47986426966
242.396799340391.889932714620.2437509723882.81519372170.001621826627881.069728817770.0189755506102-0.0894341080622-0.595275640720.0711237832211-0.0216719279703-0.4416503888880.0217957245024-0.05265716572250.06849307149020.3567192021420.00987002687010.05728482874410.370768468724-0.002557436209340.48318223058851.4459049444-51.667192111-0.898953238926
252.450128798280.830962453734-0.1245535754565.82054675609-1.267442556841.73764130199-0.00344845742435-0.251539123992-0.421732803390.3715551354570.120853158678-0.418564543510.01794466916320.0292164443143-0.08699365803540.3547040507270.01128073265350.0004479440729070.3599090351950.03708725461240.43287237970349.8965127587-52.2409016767.83050610526
263.41411901826-0.01628005118730.2180790764324.934685141792.86901433019.845158675640.0817418524564-0.20393049354-0.9374717275440.5164383858570.0892810974704-0.5494618968790.5796830848850.128338249459-0.2468988632720.422007716214-0.00214674752691-0.02089709343790.384387920950.08929808342390.79727482485551.5768541279-70.25502786765.79834228845
273.910499723-4.13263660412-3.783760603744.494942093244.85800245339.37316242030.2096683188730.49295828813-2.11792652256-0.844291184402-0.1671556197560.7997184884810.15400787264-0.7032922746290.09254449481350.62033308958-0.0332097969618-0.09072035583480.421537394276-0.03430953157440.99304138821443.5827546047-75.7237779094-3.35216450138
286.69427762873-1.38437265190.5933292544863.89151081097-1.068037317673.143939520690.170902616963-0.449262170574-1.433036576130.246364757162-0.1348811159820.1464133898010.2863160940480.1915720204280.02868214603110.54942511771-0.0157789851136-0.04048659234650.412918646370.1024545454060.97465735987445.9791815994-76.26571305278.0094628938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 156 )
6X-RAY DIFFRACTION6chain 'A' and (resid 157 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 195 )
8X-RAY DIFFRACTION8chain 'A' and (resid 196 through 209 )
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 12 )
10X-RAY DIFFRACTION10chain 'B' and (resid 13 through 32 )
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 55 )
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 87 )
13X-RAY DIFFRACTION13chain 'B' and (resid 88 through 108 )
14X-RAY DIFFRACTION14chain 'B' and (resid 109 through 136 )
15X-RAY DIFFRACTION15chain 'B' and (resid 137 through 146 )
16X-RAY DIFFRACTION16chain 'B' and (resid 147 through 164 )
17X-RAY DIFFRACTION17chain 'B' and (resid 165 through 180 )
18X-RAY DIFFRACTION18chain 'B' and (resid 181 through 195 )
19X-RAY DIFFRACTION19chain 'B' and (resid 196 through 209 )
20X-RAY DIFFRACTION20chain 'C' and (resid 0 through 12 )
21X-RAY DIFFRACTION21chain 'C' and (resid 13 through 55 )
22X-RAY DIFFRACTION22chain 'C' and (resid 56 through 87 )
23X-RAY DIFFRACTION23chain 'C' and (resid 88 through 108 )
24X-RAY DIFFRACTION24chain 'C' and (resid 109 through 126 )
25X-RAY DIFFRACTION25chain 'C' and (resid 127 through 164 )
26X-RAY DIFFRACTION26chain 'C' and (resid 165 through 180 )
27X-RAY DIFFRACTION27chain 'C' and (resid 181 through 191 )
28X-RAY DIFFRACTION28chain 'C' and (resid 192 through 205 )

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