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- PDB-6pub: Crystal Structure of the Type B Chloramphenicol Acetyltransferase... -

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Basic information

Entry
Database: PDB / ID: 6pub
TitleCrystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the Complex with Crystal Violet
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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
CRYSTAL VIOLET / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKim, Y. / Maltseva, N. / Kuhn, M. / 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
CitationJournal: To Be Published
Title: Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the Complex with Crystal Violet
Authors: Kim, Y. / Maltseva, N. / Kuhn, M. / Stam, J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,16415
Polymers23,8461
Non-polymers1,31814
Water1,49583
1
A: Chloramphenicol acetyltransferase
hetero molecules

A: Chloramphenicol acetyltransferase
hetero molecules

A: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,49245
Polymers71,5373
Non-polymers3,95542
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area21450 Å2
ΔGint-591 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.255, 83.255, 161.812
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-306-

SO4

21A-306-

SO4

31A-474-

HOH

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Components

#1: Protein Chloramphenicol acetyltransferase /


Mass: 23845.730 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-CVI / CRYSTAL VIOLET / Crystal violet


Mass: 372.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal, antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
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: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10 % v/v 1,4-Dioxane

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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 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 13030 / % possible obs: 98.9 % / Redundancy: 12 % / Biso Wilson estimate: 40.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.132 / Net I/σ(I): 20.5
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 621 / CC1/2: 0.772 / % possible all: 99

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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: 2.43→43.19 Å / SU ML: 0.2643 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9881
RfactorNum. reflection% reflection
Rfree0.2552 593 4.55 %
Rwork0.2105 --
obs0.2124 13029 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.6 Å2
Refinement stepCycle: LAST / Resolution: 2.43→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 73 83 1817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151786
X-RAY DIFFRACTIONf_angle_d0.40392431
X-RAY DIFFRACTIONf_chiral_restr0.0461239
X-RAY DIFFRACTIONf_plane_restr0.0029309
X-RAY DIFFRACTIONf_dihedral_angle_d12.3687994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.680.29691390.27393035X-RAY DIFFRACTION99.34
2.68-3.060.29341460.24783049X-RAY DIFFRACTION99.56
3.06-3.860.2391530.20833090X-RAY DIFFRACTION99.33
3.86-43.190.24261550.18383262X-RAY DIFFRACTION97.91
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)
14.037988935030.519796788503-0.1805543468881.57296018788-0.3504293012660.199180425274-0.08170972932761.189153610140.335188255478-0.2706364319920.140747889469-0.2941263518330.6081897648680.1206685407070.08981821399540.6521026558620.03702392653230.03352882904560.7699938530590.1405771343440.4348797626556.55446063871-29.9690425038-34.5259825715
22.583378755080.9685965484461.446242643222.017575489680.4505542185942.39404251883-0.2330294158770.3218039653490.480302670411-0.1777339777210.1549268648580.187324212084-0.4980126256720.3131679044270.04956085658350.4622631880610.03604765744320.01476207730310.3567122728630.06695424733110.305182494885-10.8921442489-29.9668653519-29.0001287051
31.753667826670.5418482716720.1645371180212.2221002855-0.1409466981282.30672461320.2912636123290.938114575304-0.104412112202-0.371586431592-0.0556128250330.339911796146-0.23440849699-0.534187030532-0.236720114220.4308070826880.0393747871132-0.0289303779840.4636919224850.03754156436420.325487637899-13.7582753083-40.4966749092-28.9119071093
40.297499264870.0676793153379-0.3123726333711.2251203594-0.2049559734370.509227982790.05871459967240.0163906882747-0.013263548841-0.2032564122210.002630847934620.2540176539670.0701558236459-0.167379172355-0.102211085080.3077808909570.000796759435689-0.04928050639140.4009422663890.05895795609080.390005163241-15.6821107969-45.2694248449-19.4671595717
54.170936411592.813714321580.1614747282558.47946935548-0.4618286101531.838872802950.06241115430070.0890323648295-0.0135402206596-0.4530507945210.3204967229860.8173770546630.413562308769-0.291927800894-0.2929703339830.375074936234-0.0476724591937-0.1096912088520.539812939170.05789084427840.423831573442-27.7098046169-56.7225756487-22.6908847545
61.7109737156-0.234371837271.005519120212.222085450530.2549047859951.331657562640.13990645057-0.02213847200370.07194502666580.130294820175-0.03013869413580.0828826577751-0.190958983815-0.147371184586-0.1233062183920.26979755215-0.01894377343220.04025076732950.308031349250.0487521791010.244119692319-7.53301774742-36.0045640507-13.6054132447
73.45344781682-0.8793809222120.07706495318854.586521717541.55675925522.44969712560.136724372907-0.2596828298510.597487594689-0.1148789386430.0583673768231-0.19469723611-0.33504917922-0.000685579531436-0.2114172303150.2975154979050.0405945768320.07537753197390.3105644364140.009358166704030.288538248234-5.89082113624-24.1515998676-4.66718372475
83.2085411842-0.341310948595-1.894425264126.70512825087-4.308689351976.399562008920.2726274117430.7929731332671.02009487894-0.7750211296670.606577386909-0.130979501856-0.899884007042-0.670774789888-0.8133853880630.6507318525340.06958601307570.1584643137430.4197092989790.1055673886310.572798823961-8.63140078706-12.6416808099-19.0141297555
92.58190629074-0.622861648341-1.198741146075.729241048211.714999729266.607498152750.279963710178-0.1780787032211.006787225460.02056454392450.463148122434-0.318233652969-1.253198938920.315656066617-0.6631779804530.606469569437-0.03989634544870.1399236174870.276539591237-0.01319982996610.623099184797-3.77237324157-10.7185838947-10.2595090519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 108 )
6X-RAY DIFFRACTION6chain 'A' and (resid 109 through 156 )
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 174 )
8X-RAY DIFFRACTION8chain 'A' and (resid 175 through 186 )
9X-RAY DIFFRACTION9chain 'A' and (resid 187 through 207 )

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