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- PDB-6pu9: Crystal Structure of the Type B Chloramphenicol O-Acetyltransfera... -

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Basic information

Entry
Database: PDB / ID: 6pu9
TitleCrystal Structure of the Type B Chloramphenicol O-Acetyltransferase from Vibrio vulnificus
ComponentsAcetyltransferase
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
Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKim, Y. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / 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 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 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: Acetyltransferase
B: Acetyltransferase
C: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4257
Polymers71,2043
Non-polymers2224
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-52 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.457, 71.457, 108.635
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Acetyltransferase


Mass: 23734.613 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (bacteria)
Strain: CMCP6 / Gene: VV2_0610 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: A0A3Q0KYH6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 8 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 65032 / % possible obs: 95.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 24.72 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.054 / Net I/σ(I): 19.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.245 / Num. unique obs: 2229 / CC1/2: 0.949 / % possible all: 65.8

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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: 1.7→40.82 Å / SU ML: 0.2155 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 32.5973
RfactorNum. reflection% reflection
Rfree0.2411 3144 4.85 %
Rwork0.1943 --
obs0.1965 64803 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.89 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 13 311 5060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585008
X-RAY DIFFRACTIONf_angle_d0.76376796
X-RAY DIFFRACTIONf_chiral_restr0.059681
X-RAY DIFFRACTIONf_plane_restr0.005898
X-RAY DIFFRACTIONf_dihedral_angle_d15.78382910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.2962840.28991890X-RAY DIFFRACTION64.47
1.73-1.760.3757890.28572257X-RAY DIFFRACTION75.14
1.76-1.790.32341700.28022515X-RAY DIFFRACTION86.39
1.79-1.820.28131630.26892755X-RAY DIFFRACTION96.14
1.82-1.850.31321440.27662919X-RAY DIFFRACTION98.2
1.85-1.890.30521680.24692891X-RAY DIFFRACTION99.19
1.89-1.930.26491280.23232999X-RAY DIFFRACTION99.62
1.93-1.980.28661530.22422853X-RAY DIFFRACTION99.37
1.98-2.030.25821100.22542995X-RAY DIFFRACTION99.3
2.03-2.080.25671360.22042827X-RAY DIFFRACTION96.67
2.08-2.140.24841590.19592906X-RAY DIFFRACTION99.55
2.14-2.210.27161780.19262911X-RAY DIFFRACTION99.29
2.21-2.290.2361620.19162951X-RAY DIFFRACTION99.55
2.29-2.380.26391410.19062927X-RAY DIFFRACTION99.42
2.38-2.490.25971660.18752837X-RAY DIFFRACTION98.33
2.49-2.620.22551550.20072911X-RAY DIFFRACTION98.87
2.62-2.790.20171460.19692919X-RAY DIFFRACTION98.84
2.79-30.2591310.20132950X-RAY DIFFRACTION99.04
3-3.310.24311360.18852901X-RAY DIFFRACTION98.57
3.31-3.780.22831230.18572948X-RAY DIFFRACTION99.13
3.78-4.770.20861190.16442795X-RAY DIFFRACTION94.06
4.77-40.820.22061830.16912802X-RAY DIFFRACTION96.76
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)
11.83878046822-0.7170961114321.00486849580.4357128493550.07162431052622.093030315020.06167118977170.676275802005-0.147833590367-0.608831770639-0.2824975539980.1484604656840.2384552521730.1464757352550.2763958261130.417610631363-0.016024622086-0.01698873332470.308872226335-0.04658409390880.24583195101919.04174286940.686502344425-9.63191962396
26.384278785471.44039347361-0.5677725189265.67112931004-0.3556221010133.564340662430.1857783236980.345811958105-0.223641340819-0.515819041787-0.495658842573-0.850814858070.3462019886810.2394130458610.176660051390.403471846770.06407826782210.08176973478960.3538741110210.1155501861990.42306831071637.06830084560.421165554495-7.9424918052
32.590482412790.8471817508030.7132284713291.815037822730.3962302461730.634304658184-0.03918585411720.0844586562691-0.345445785125-0.1614371953740.0495782437717-0.1793956741740.04513666882960.123460064149-0.02948715887770.282470544301-0.01125032477490.01085202327630.2495340279430.01775794382870.29143446611934.30724390166.01904677115-0.294731257489
48.498081725554.96897422599-2.463717819166.10022655693-1.592383608552.81803237823-0.2693861051160.476127829166-0.252044208394-0.7734325282330.328415224538-0.8154051629890.2321950086860.391979540891-0.07721422006890.306259121237-0.03874708581970.1109431765730.417013079111-0.03890494411610.40962224720150.1005582829.15917882576-4.44344710715
52.624527740711.12544331634-0.1051203571614.08959697731-0.03375430200610.5332222549150.054190505225-0.129426659023-0.6149466870580.191923332998-0.0870226451620.154158208330.113267968508-0.03737255278890.02075731077640.290768300162-0.0363892951054-0.005950457962070.212371118860.04359430891410.29884347923917.4523283739-4.911442039726.66118118468
62.541561257010.835801229411.718795184011.7579735505-0.006894293692412.162361680650.539464947784-0.45436866448-0.5785262822870.08590193198130.1064387418050.8446101781750.698216288193-0.380678813241-0.3188139467210.502899849716-0.0764158579119-0.05291989744050.3183829550740.1816920335560.8203793414648.63748926365-21.96183426389.21634682978
76.818317969153.249779070010.4504305165394.54378468869-0.5200025516043.46887161696-0.6646899379930.9147769508750.305361845177-1.303437882780.244429416437-0.567351280565-0.4891009549350.3089689969420.2494822067140.671940358046-0.03828593581310.06070600362470.479546089309-0.02014836697720.4886104861917.8659082349728.2708798413-10.8366473477
85.611349578430.646656460185-0.2203827799895.333079665730.7584000883013.22788729169-0.08084409082810.818485192123-0.45011884634-0.3477131552960.0833359311825-0.06619202017040.202046202956-0.01698958226890.01513377980210.2871323828910.00242167427824-0.0120020881080.331163081224-0.01586545970740.2443095428415.120832188418.8824631614-8.28833943203
91.34488688757-0.5552663179030.2563922860773.63348489025-0.7261286520570.4661860888280.109928639755-0.00846580695669-0.354895789323-0.2337010295470.05858910600870.5649209396840.0602015188871-0.0315385730431-0.1783085956680.27813702977-0.03701494200060.01738955379910.239943826591-0.02741064757530.3245498478237.7917890871511.2559351762-0.332861133477
100.374930511821-0.354206115276-0.3036139333499.223258663842.415023160711.517138293230.2294692818610.300627840146-0.612450759517-0.732229892634-0.07163530595121.048522232390.159291481986-0.254524386064-0.1332796425880.440048160281-0.0566022029864-0.1669677666860.333677157182-0.08461833023860.6317546987842.25103000751-4.35958616957-4.30071016556
112.33566273841-1.255591891910.2863327715343.179804063460.5905244993851.242124747430.0177357762547-0.040708416139-0.2021698024630.08756789583250.01971043600980.328556851267-0.0163348099034-0.160725590149-0.06134706219650.230605510328-0.01051171970550.06023552971990.1917578217710.001296096838980.2440747418749.282965790822.87482887744.38744827134
124.29302203217-1.857145622650.3509241021574.558505784260.03621015330050.778575211264-0.0765831843746-0.2492784829990.5790198760460.2990094423810.1342043434540.626551420815-0.158956446621-0.105924251481-0.04711042144290.310768672879-0.02231589001920.1071601423580.24902016197-0.04119421446430.4487169889154.6248954554936.453320028.1979895498
131.91573308138-0.1299302531442.035140416825.37420090408-0.9242754243887.03959069340.170133536408-0.2392407588811.201640969170.1352441523650.01581109680470.306636348842-0.764556042693-0.829159848521-0.06930997528780.4405486604240.08211885591280.1969044458970.39968300815-0.008085692984220.809979186895-4.037434969947.10943937899.15123979899
144.47084046012-1.647998699590.8537385659725.50168233102-3.000997355021.635742306230.2600609754610.931275610383-0.831183647077-1.59493432517-0.6664075167980.0806213538540.206483242298-0.08102843103560.3102685649990.60115310156-0.006119813810320.009100976353640.520827555552-0.07352539032770.20326605371739.202992895724.3455937336-10.9919754668
154.50183311465-0.458504999417-0.4811721827752.602743175030.4370043444391.58106440304-0.03413386663910.4434556748890.272107514645-0.424751081878-0.04708115127030.182289154448-0.149389357599-0.07354858118110.02384539313990.380069035275-0.0347770349122-0.02451626593380.3388129924530.05384161957530.18667551076432.874477083627.4221965904-9.56163010348
163.82053910673-0.372117264828-0.6097992420040.940472800389-0.03181153855650.5116654702110.1544001177130.1197404373260.5181669948860.0330630909535-0.02746529574180.0155948699297-0.0391905759142-0.00532609046745-0.06435400681790.312639493141-0.0292214973174-0.002510678545210.274351259033-0.002630540650310.23397228515225.056228556231.6209735363-0.213861630568
176.85371783361-2.521322186670.4139220866713.26456469268-0.3421345610081.011736284580.1427155749110.7308286432351.46159710417-0.165557501646-0.1041959057880.44181877265-0.237984128808-0.202992540209-0.0623335120850.3927828147890.01951332306050.0513573439610.3468002067660.2006229047460.64369853841314.393512340843.8771853147-4.21158546747
183.339388582180.8487129579860.2632010339831.923809912870.0722942956960.7325019508170.0176821640734-0.252153083760.002975168946030.170633610459-0.107294641234-0.279129376721-0.04930912862710.07041495059460.09544433643870.262805919257-0.0439061959766-0.02804804248280.2304206357930.02340247882010.11883132146442.960038665922.41412174976.36995470293
199.473162237652.988224647870.2953381345368.784280634080.6348255333564.526732373880.0653455481036-0.552468525309-0.9289855631170.434215124340.140085217308-1.045423510240.2027609374140.36736666559-0.09391391388350.303818104-0.0615518819183-0.1161738336180.4158253886390.09500621576220.384038867362.271843162923.21790819798.98653498411
202.98256811512-1.833826860460.2402123555643.425660024490.4738710662392.124233503740.04609749780571.465179089380.024861093854-0.595123472979-0.3605476357070.6670161550660.0525956856752-0.4858241499930.1428249579650.526416238494-0.0306791539821-0.02413563868810.567018399782-0.07406092408240.34077730421420.8418767671-2.66087848178-10.9563380502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 25 through 42 )
2X-RAY DIFFRACTION2chain 'C' and (resid 43 through 55 )
3X-RAY DIFFRACTION3chain 'C' and (resid 56 through 87 )
4X-RAY DIFFRACTION4chain 'C' and (resid 88 through 108 )
5X-RAY DIFFRACTION5chain 'C' and (resid 109 through 195 )
6X-RAY DIFFRACTION6chain 'C' and (resid 196 through 207 )
7X-RAY DIFFRACTION7chain 'A' and (resid 6 through 24 )
8X-RAY DIFFRACTION8chain 'A' and (resid 25 through 55 )
9X-RAY DIFFRACTION9chain 'A' and (resid 56 through 87 )
10X-RAY DIFFRACTION10chain 'A' and (resid 88 through 108 )
11X-RAY DIFFRACTION11chain 'A' and (resid 109 through 146 )
12X-RAY DIFFRACTION12chain 'A' and (resid 147 through 195 )
13X-RAY DIFFRACTION13chain 'A' and (resid 196 through 207 )
14X-RAY DIFFRACTION14chain 'B' and (resid 6 through 24 )
15X-RAY DIFFRACTION15chain 'B' and (resid 25 through 55 )
16X-RAY DIFFRACTION16chain 'B' and (resid 56 through 87 )
17X-RAY DIFFRACTION17chain 'B' and (resid 88 through 108 )
18X-RAY DIFFRACTION18chain 'B' and (resid 109 through 195 )
19X-RAY DIFFRACTION19chain 'B' and (resid 196 through 207 )
20X-RAY DIFFRACTION20chain 'C' and (resid 6 through 24 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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