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- PDB-5vd6: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -

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Basic information

Entry
Database: PDB / ID: 5vd6
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with bisubstrate analog 6
Componentsacetyltransferase PA4794
Keywordstransferase/transferase inhibitor / GNAT / acetyltransferase / bisubstrate inhibitor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-93P / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsMajorek, K.A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094585 United States
CitationJournal: FEBS Lett. / Year: 2017
Title: Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases.
Authors: Reidl, C. / Majorek, K.A. / Dang, J. / Tran, D. / Jew, K. / Law, M. / Payne, Y. / Minor, W. / Becker, D.P. / Kuhn, M.L.
History
DepositionApr 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: acetyltransferase PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6498
Polymers18,0011
Non-polymers1,6487
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.088, 76.151, 38.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein acetyltransferase PA4794


Mass: 18000.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4794 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HV14
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-93P / (3R,5S,9R,23S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14-dioxo-23-({[(phenylacetyl)amino]acetyl}amino)-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatetracosan-24-oic acid 3,5-dioxide (non-preferred name)


Mass: 1071.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H56N9O20P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulfate, 0.1M Bis Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 53381 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Rrim(I) all: 0.074 / Χ2: 1.787 / Net I/σ(I): 9.9 / Num. measured all: 325622
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.225.50.64426390.8520.2970.7120.72797.8
1.22-1.2460.5925810.8670.2580.6450.73398.1
1.24-1.276.20.53226060.8840.230.580.77198.3
1.27-1.296.20.46626120.9050.20.5080.79998.5
1.29-1.326.20.39626200.9260.170.4320.82798.7
1.32-1.356.20.34726340.9510.1490.3790.86498.6
1.35-1.396.20.29326330.960.1260.3190.91598.6
1.39-1.426.20.25826180.9620.1110.2810.95999.3
1.42-1.466.20.21226740.9770.0910.2321.07598.8
1.46-1.516.30.1826430.9820.0780.1961.23199.5
1.51-1.576.30.15526650.9840.0670.171.38899.3
1.57-1.636.30.12926450.9890.0560.1411.50299.4
1.63-1.76.30.11326890.9910.0490.1241.70399.6
1.7-1.796.20.126780.9910.0440.112.1399.7
1.79-1.96.20.08626960.9930.0370.0942.45799.6
1.9-2.056.10.07527140.9940.0330.0823.0699.9
2.05-2.266.10.06526940.9960.0290.0713.30899.6
2.26-2.596.10.05927350.9960.0260.0653.40599.7
2.59-3.265.90.05327510.9970.0230.0583.63599.4
3.26-505.30.05328540.9950.0240.0594.24497.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-3000data scaling
HKL-2000data collection
PDB_EXTRACT3.22data extraction
MOLREPphasing
HKL-3000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L8A

4l8a


Resolution: 1.2→45.68 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.1292 / FOM work R set: 0.9066 / SU B: 1.097 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0348 / SU Rfree: 0.0361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1632 2630 4.9 %RANDOM
Rwork0.1324 ---
obs0.1339 50722 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.43 Å2 / Biso mean: 17.654 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.2→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 100 251 1594
Biso mean--26.41 32.2 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191435
X-RAY DIFFRACTIONr_bond_other_d0.0020.021281
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9621963
X-RAY DIFFRACTIONr_angle_other_deg1.98232957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75822.81364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51115212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2321513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211697
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02312
X-RAY DIFFRACTIONr_rigid_bond_restr9.33731431
X-RAY DIFFRACTIONr_sphericity_free23.0385159
X-RAY DIFFRACTIONr_sphericity_bonded9.16751477
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 187 -
Rwork0.218 3614 -
all-3801 -
obs--96.47 %

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