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- PDB-7kye: Structure of a GNAT superfamily PA3944 acetyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 7kye
TitleStructure of a GNAT superfamily PA3944 acetyltransferase in complex with CHES
ComponentsAcetyltransferase PA3944
KeywordsTRANSFERASE / PA3944 / acetyltransferase / GNAT Superfamily / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Acyl-CoA N-acyltransferase / COENZYME A / Acetyltransferase PA3944
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCzub, M.P. / Porebski, P.J. / Cymborowski, M. / Minor, W. / 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: Structure of a GNAT superfamily PA3944 acetyltransferase in complex with CHES
Authors: Czub, M.P. / Porebski, P.J. / Cymborowski, M. / Minor, W.
History
DepositionDec 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1795
Polymers22,0801
Non-polymers1,0994
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.208, 44.075, 97.313
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetyltransferase PA3944 / GCN5-related N-acetyltransferase / GNAT


Mass: 22080.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3944 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HX72, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.2 uL of 20 mg/mL protein incubated with 2.5 mM CoA was mixed with 0.2 uL of the well condition (20%w/v PEG 8K, 100mM CHES pH=9.5 (Emerald - Wizard Full (I & II) #1) and equilibrated ...Details: 0.2 uL of 20 mg/mL protein incubated with 2.5 mM CoA was mixed with 0.2 uL of the well condition (20%w/v PEG 8K, 100mM CHES pH=9.5 (Emerald - Wizard Full (I & II) #1) and equilibrated against well solution in 96 Well 3 drop Crystallization Plate (Swissci).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 13814 / % possible obs: 94.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.054 / Rrim(I) all: 0.147 / Χ2: 1.104 / Net I/σ(I): 7.9 / Num. measured all: 84478
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.963.70.5125540.8360.2660.5810.82378.7
1.96-23.90.4746070.7990.2460.5380.78884.4
2-2.0440.4455910.9090.230.5050.82884.5
2.04-2.084.10.4176220.8610.210.470.81687.2
2.08-2.124.30.4876360.850.2430.5480.84188
2.12-2.174.50.4596440.8610.2240.5140.82889.9
2.17-2.234.70.416530.9040.1920.4560.92293.3
2.23-2.294.90.4836910.8860.2210.5340.86695.2
2.29-2.365.30.546900.9030.2360.5920.91797.2
2.36-2.4360.5147100.9360.2160.560.89597.9
2.43-2.526.40.517100.9310.2090.5530.894100
2.52-2.6270.537240.9590.2090.5710.93899.7
2.62-2.747.50.4847330.9640.1870.520.914100
2.74-2.887.80.3777220.960.1450.4050.946100
2.88-3.0680.2787260.9890.1050.2981.048100
3.06-3.37.90.2077310.9940.0790.2221.13100
3.3-3.637.80.1217500.9960.0460.131.301100
3.63-4.167.80.0857320.9970.0330.0921.521100
4.16-5.247.60.0717630.9970.0270.0761.599100
5.24-506.60.0668250.9970.0280.0721.83899.3

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EDD

6edd


Resolution: 1.93→32.69 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.579 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 659 4.8 %RANDOM
Rwork0.1735 ---
obs0.1753 13113 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.93 Å2 / Biso mean: 49.043 Å2 / Biso min: 29.98 Å2
Baniso -1Baniso -2Baniso -3
1-4.7 Å2-0 Å20 Å2
2---3.08 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 1.93→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 69 91 1647
Biso mean--54 52.05 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131611
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171469
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.6632194
X-RAY DIFFRACTIONr_angle_other_deg1.11.5773361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.13218.879107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11915232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6661522
X-RAY DIFFRACTIONr_chiral_restr0.0480.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
LS refinement shellResolution: 1.931→1.981 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 38 -
Rwork0.28 773 -
all-811 -
obs--77.68 %
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)
19.5192-1.4683-3.03015.4318-1.42848.0810.0812-0.09390.19420.9909-0.1368-1.00330.35741.00470.05560.61790.0058-0.16120.39990.03520.467415.779-2.4220.488
24.0507-0.73121.77322.0633-0.36883.09420.02930.4239-0.03850.1752-0.14840.14860.2072-0.05620.1190.0798-0.02750.04540.2736-0.01170.26344.1161.0384.571
312.36441.55676.1365.93113.42976.6466-0.02360.41950.48540.18350.0154-0.18430.03370.11140.00830.05660.01240.01510.26570.03580.250117.3194.454.498
41.67121.742-0.9245.6817-0.53071.04410.01260.0725-0.03740.41770.0073-0.16750.0620.1259-0.01990.108-0.0084-0.03060.19360.01190.203312.9726.19512.795
53.37222.1801-0.77474.7722-0.24760.58860.0513-0.02650.10710.9773-0.019-0.00940.05650.1187-0.03240.3101-0.0234-0.00960.17270.00290.20099.2526.96418.871
68.9179-0.71472.00193.8181-0.18493.9949-0.0362-0.2116-0.04550.7484-0.0042-0.26550.11180.23940.04030.2302-0.0167-0.03070.1751-0.01560.207713.37615.66617.009
72.2540.6864-0.24574.6733-0.51753.69270.10020.28190.13790.3976-0.05470.3256-0.1683-0.1418-0.04550.0991-0.00460.06490.1884-0.02910.25545.02120.92312.629
85.19625.95225.640617.8960.20249.74380.6124-1.30210.40792.3293-0.88230.4745-0.0588-1.70680.26991.0651-0.0063-0.18290.6589-0.10730.512613.80415.67529.231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 19
2X-RAY DIFFRACTION2A20 - 52
3X-RAY DIFFRACTION3A53 - 67
4X-RAY DIFFRACTION4A68 - 97
5X-RAY DIFFRACTION5A98 - 130
6X-RAY DIFFRACTION6A131 - 145
7X-RAY DIFFRACTION7A146 - 183
8X-RAY DIFFRACTION8A184 - 192

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