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- PDB-12jc: Crystal Structure of Thialysine Acetyltransferase from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 12jc
TitleCrystal Structure of Thialysine Acetyltransferase from Pseudomonas aeruginosa
ComponentsThialysine Acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferase (GNAT) / polyamine acetyltransferase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology: / N-acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Probable N-acetyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Kuhn, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
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 Putative L-amino Acid N-acyltransferase MnaT from Pseudomonas aeruginosa
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Kuhn, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionApr 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Structure summary / Category: entity / struct / struct_keywords
Item: _entity.pdbx_description / _struct.title ..._entity.pdbx_description / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thialysine Acetyltransferase
B: Thialysine Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9905
Polymers36,8042
Non-polymers1863
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-37 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.467, 52.303, 59.012
Angle α, β, γ (deg.)90.000, 95.160, 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
11B-445-

HOH

21B-452-

HOH

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Components

#1: Protein Thialysine Acetyltransferase


Mass: 18401.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0478 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9I640
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.5, 25 % (w/v) PEG3350

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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 X 6M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28294 / % possible obs: 95.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.75 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.108 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4 / Num. unique obs: 978 / CC1/2: 0.876 / Rrim(I) all: 0.376 / % possible all: 67.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.82 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 20.7686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2041 1328 4.7 %
Rwork0.1635 26950 -
obs0.1654 28278 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 12 282 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832649
X-RAY DIFFRACTIONf_angle_d0.87743596
X-RAY DIFFRACTIONf_chiral_restr0.0597376
X-RAY DIFFRACTIONf_plane_restr0.0121476
X-RAY DIFFRACTIONf_dihedral_angle_d14.5824991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.2497980.22382250X-RAY DIFFRACTION71.76
1.87-1.960.27621540.18352766X-RAY DIFFRACTION89.71
1.96-2.060.20111550.17093103X-RAY DIFFRACTION99.85
2.06-2.190.22011640.16433114X-RAY DIFFRACTION99.79
2.19-2.360.2591460.16723114X-RAY DIFFRACTION99.39
2.36-2.590.2061620.17343097X-RAY DIFFRACTION99.88
2.59-2.970.20281570.18063118X-RAY DIFFRACTION99.63
2.97-3.740.18651480.15773162X-RAY DIFFRACTION99.58
3.74-40.820.1841440.14793226X-RAY DIFFRACTION99.59
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)
12.68718487073-0.9097668619040.6827743574022.53026279249-0.06320851232272.199398656940.382848156454-0.00471132216608-0.082265264490.393116683554-0.27608379420.05692663925240.2177024846240.343491460706-0.05100920320770.327416635489-0.0506419034230.02268445803180.2194718061180.01235423945170.19746526437339.509267442-4.622006838658.0206623354
25.5691091202-0.4720965638413.782153593370.1682130464570.3830007118396.49891402699-0.0558364114844-0.306323870802-0.7287511911160.726589511325-0.0359776974802-0.215061148964-0.4597162101380.4057647686220.170230434070.548397000420.0230314213857-0.002205072614250.2917893270560.1121807754560.31943690360534.914712459-15.517502120516.7582666843
32.07524061595-1.59130578653-0.302084448012.978337389290.04846935125230.756901701340.3231441179430.465226756867-0.115333792716-0.40296125751-0.4190423381650.251811382563-0.0608599920113-0.2469605342070.103697140380.3178580866350.0810512695799-0.04172343644720.275458827977-0.07510582737360.24517779840927.523860687-9.3324474241.21360571165
42.63972992792-0.19431873906-0.5287316298530.7704067463360.3045560426431.430184844090.1131861184950.2562848715650.0637506167713-0.119012959748-0.0700537069666-0.201419394582-0.08537381895440.151591965214-0.05259431321860.161977939326-0.01905625655040.02617627436660.1685633511460.002468822795110.21207009651233.28347952192.338586146716.88650414415
52.77268151843-0.684227115582-0.02928411804811.047704277830.4662052243810.738016878372-0.1198491162820.029180616083-0.09669714193140.2004775541490.0047332182550.00672902240272-0.082468840508-0.08999938138210.1118752439720.188834015917-0.01302273448410.002587401396980.1562313609890.01243311375360.14031454343523.94168551226.0767265336314.0354072118
62.06351234432-0.0770013946585-0.04123382663076.28295424545-1.418100325633.31965933924-0.14531063352-0.09684299163010.4638722387830.3571845063040.159351243792-1.08893645-0.1452283109410.5440524388390.003975970504680.213710688153-0.030055973521-0.1083191785190.42998173618-0.01375311146340.40384023719147.64061752022.1088000968713.8834611855
75.59146671157-2.305285839290.9220077689062.08431379656-0.5708884430271.98930425892-0.007373504193430.06537137348850.481384150844-0.402102644965-0.0516738459566-0.485650811096-0.4046155094390.08515757069150.0005184645684930.268964475235-0.0322954553840.07856767623240.1614121144010.01920140565270.29091087655933.49819655811.73115922288.59382490004
81.99137926966-0.07752438609060.3365446245292.0968163112-0.4304191092872.8889144680.0549341257312-0.2279028722360.02818430242420.03137405082130.124353830692-0.123899122056-0.0486375380016-0.11006760128-0.1192687263290.2350740841570.00646349641208-0.009857058178410.177969369979-0.007161327128030.19055153343327.39839615045.9150950296518.9475170161
91.558370706110.454387769313-0.04160927909731.4737196454-0.1876011701010.850623157061-0.109572358304-0.1589940435580.05735925763080.1386281166570.136509711531-0.170212316908-0.0651511767160.094830397621-0.0346370335610.213586977880.0102988741303-0.03111588249690.187332727682-0.02532028564210.21991385026227.49309119114.3583093387624.9749424817
101.28950734680.173852693742-0.3009298045933.17527940737-0.9619596111492.841757686250.1428554138460.0595958141646-0.873363279875-0.009945461987250.3575839118360.3702017403390.733325898325-0.181235364275-0.04695345515610.55861767762-0.0698717469507-0.1726016311230.1304395885650.005938787276330.59846208809910.7832046657-17.894045101718.6776260054
112.52787282960.251275977522-0.1697939636032.99886180838-0.8070523025821.625735609310.03376663359450.04705013384380.1709509038590.149704333729-0.09975926745070.0478755402512-0.134765152637-0.323255116650.05183117055360.183716463876-0.0160407372947-0.01886405244680.264161166787-0.01221566499810.1677140223033.47130344488.4921749852313.5742623458
123.22232888325-0.707806839459-0.1938620867131.17099063319-0.2440534264941.844941541770.126196040691-0.100473896238-0.315121474759-0.012648099831-0.05121711485330.1171494573660.186013623549-0.334247946048-0.06579360444050.174819359265-0.0676322600483-0.02019070768760.2026051959390.006537557537650.1725928008868.688377565-3.947432444516.2444118014
132.404468763880.192365566439-0.5018678398861.8919020247-0.6974959330371.479807229690.0163625496962-0.146359936405-0.008262149053170.1497055881980.01772665289250.0661586755629-0.147812076346-0.0111099889924-0.01217151137380.2157516032210.03581005386820.001826335749290.170458850475-0.01858947434640.15412910686219.60883690241.1692207838923.2192896355
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 27 )AA2 - 271 - 26
22chain 'A' and (resid 28 through 36 )AA28 - 3627 - 35
33chain 'A' and (resid 37 through 50 )AA37 - 5036 - 49
44chain 'A' and (resid 51 through 73 )AA51 - 7350 - 72
55chain 'A' and (resid 74 through 88 )AA74 - 8873 - 87
66chain 'A' and (resid 89 through 96 )AA89 - 9688 - 95
77chain 'A' and (resid 97 through 111 )AA97 - 11196 - 110
88chain 'A' and (resid 112 through 125 )AA112 - 125111 - 124
99chain 'A' and (resid 126 through 149 )AA126 - 149125 - 148
1010chain 'A' and (resid 150 through 158 )AA150 - 158149 - 157
1111chain 'B' and (resid 2 through 60 )BD2 - 601 - 59
1212chain 'B' and (resid 61 through 111 )BD61 - 11160 - 110
1313chain 'B' and (resid 112 through 158 )BD112 - 158111 - 157

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