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- PDB-4kub: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -

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Basic information

Entry
Database: PDB / ID: 4kub
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with CoA
ComponentsGNAT superfamily acetyltransferase PA4794
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / GNAT / acetyltransferase
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
COENZYME A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMajorek, K.A. / Chruszcz, M. / Osinski, T. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural, functional, and inhibition studies of a Gcn5-related N-acetyltransferase (GNAT) superfamily protein PA4794: a new C-terminal lysine protein acetyltransferase from pseudomonas aeruginosa.
Authors: Majorek, K.A. / Kuhn, M.L. / Chruszcz, M. / Anderson, W.F. / Minor, W.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2May 7, 2014Group: Database references
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GNAT superfamily acetyltransferase PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,62113
Polymers18,0011
Non-polymers1,62012
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GNAT superfamily acetyltransferase PA4794
hetero molecules

A: GNAT superfamily acetyltransferase PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,24226
Polymers36,0012
Non-polymers3,24124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7080 Å2
ΔGint-70 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.359, 76.796, 39.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

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Components

#1: Protein GNAT superfamily acetyltransferase PA4794


Mass: 18000.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4794 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9HV14
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
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: 19-BM / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 16, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. all: 25056 / Num. obs: 25056 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 37.1
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1214 / Rsym value: 0.79 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000MOLREPphasing
REFMAC5.7.0029refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→39.34 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17837 1278 5.1 %RANDOM
Rwork0.14273 ---
all0.1445 23744 --
obs0.1445 23744 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.57→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 97 215 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191541
X-RAY DIFFRACTIONr_bond_other_d00.021436
X-RAY DIFFRACTIONr_angle_refined_deg2.1112.052112
X-RAY DIFFRACTIONr_angle_other_deg3.57433286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3575187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67822.60969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84715232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7161515
X-RAY DIFFRACTIONr_chiral_restr0.1310.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211725
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02380
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.566→1.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 97 -
Rwork0.233 1591 -
obs-1591 93.62 %
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)
10.79780.5969-0.49941.2432-0.08381.55780.0368-0.0311-0.06790.0721-0.0403-0.0907-0.014-0.00680.00360.054-0.0059-0.00820.07640.00890.051612.764-13.704-0.66
20.96040.0035-0.50020.6869-0.13191.6675-0.0812-0.0104-0.10210.00490.0641-0.0288-0.0029-0.09870.0170.0483-0.025-0.00490.0669-0.00680.045814.142-15.791-9.9
31.7263-0.70.63522.1213-2.14712.9378-0.02760.1167-0.1451-0.17020.08210.04160.2205-0.0602-0.05460.0801-0.0371-0.00120.0731-0.02330.032916.522-16.921-19.829
40.5531-0.3359-0.2012.28450.71571.21780.01120.01940.00020.00240.040.02310.007-0.0613-0.05110.0622-0.0251-0.00310.07780.00150.052123.573-1.689-9.463
55.2744.31243.31715.66983.70374.9737-0.07190.3996-0.1714-0.21240.2207-0.33320.27260.171-0.14870.1285-0.02780.01210.1356-0.01690.067122.884-10.633-22.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 45
2X-RAY DIFFRACTION2A46 - 93
3X-RAY DIFFRACTION3A94 - 114
4X-RAY DIFFRACTION4A115 - 153
5X-RAY DIFFRACTION5A154 - 159

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