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

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Basic information

Entry
Database: PDB / ID: 4kua
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794
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
N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMajorek, K.A. / Chruszcz, M. / 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GNAT superfamily acetyltransferase PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,04015
Polymers18,0011
Non-polymers1,03914
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.477, 76.619, 39.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-SO4 / SULFATE ION / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
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-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 28398 / Num. obs: 28398 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 35.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1407 / Rsym value: 0.661 / % possible all: 100

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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
Starting model: 2i6c

2i6c
PDB Unreleased entry


Resolution: 1.5→39.55 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.493 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18975 1437 5.1 %RANDOM
Rwork0.15754 ---
all0.15919 26930 --
obs0.15919 26930 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 mean: 25.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.75 Å2-0 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 61 224 1537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191414
X-RAY DIFFRACTIONr_bond_other_d0.0050.021362
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9811909
X-RAY DIFFRACTIONr_angle_other_deg0.89633108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7325178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80622.72766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53815221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2531514
X-RAY DIFFRACTIONr_chiral_restr0.1260.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 99 -
Rwork0.219 1953 -
obs-1953 98.18 %
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)
12.08911.1673-0.2332.72690.11763.6386-0.04770.14680.3123-0.0059-0.02030.2734-0.3004-0.11470.06790.1849-0.02090.00150.1087-0.0060.0613.57326.80713.295
24.52364.6275-1.02147.7046-2.09091.69770.0956-0.19130.0390.0666-0.1362-0.005-0.12310.01460.04070.137-0.01940.01430.1318-0.01360.004917.44118.1121.741
35.03250.7724-1.46788.19742.91258.8008-0.05990.0921-0.13180.10060.0056-0.18690.4557-0.21880.05440.1563-0.0471-0.00460.1431-0.00310.008311.9825.4720.37
40.9986-0.19241.42451.3263-1.59323.46390.10930.1655-0.0457-0.1708-0.12130.00270.34750.41370.0120.23370.03120.02160.2775-0.00990.103721.8549.65717.903
51.6233-0.8299-0.19093.25251.50022.7884-0.02710.0420.1326-0.09410.01470.1141-0.10460.01570.01250.15-0.0273-0.00290.1509-0.00470.041114.10120.67613.182
60.25270.23180.88390.25740.8429.68730.03490.0457-0.03560.08030.0583-0.01120.23610.3082-0.09320.1442-0.01890.00970.1404-0.00990.01917.4159.3870.206
73.3421-2.74080.0012.75390.51843.1702-0.0287-0.2525-0.15840.07680.07280.3475-0.1004-0.0713-0.0440.1458-0.00470.03870.1639-0.0290.13336.26217.90318.798
83.0768-1.3612-2.44382.34223.00475.1022-0.01890.03660.1545-0.1880.04530.0009-0.25630.0689-0.02640.1548-0.0237-0.00380.11710.01380.01210.91718.9442.573
92.32390.9292-1.3511.2688-1.24851.37790.1348-0.04570.1460.11190.01410.1323-0.18690.0431-0.14890.1643-0.03460.0180.1235-0.01380.01725.2477.2577.309
105.13151.1407-0.78848.6554-0.07712.58530.08810.09910.2057-0.00020.0820.4438-0.2558-0.0674-0.170.1618-0.02520.02210.12620.02220.03720.329.9012.738
111.6222-1.07553.37842.5292-2.91687.84720.02930.0867-0.1037-0.00450.0372-0.07660.05850.1623-0.06640.12650.0013-0.01090.1123-0.00310.03557.973-4.24512.229
124.46724.9826-4.29512.0754-7.21548.00290.00450.40680.2354-0.15960.26870.3665-0.2744-0.2787-0.27320.1714-0.03220.00920.17770.02320.01545.66111.186-2.998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 10
2X-RAY DIFFRACTION2A11 - 20
3X-RAY DIFFRACTION3A21 - 32
4X-RAY DIFFRACTION4A33 - 50
5X-RAY DIFFRACTION5A51 - 68
6X-RAY DIFFRACTION6A69 - 80
7X-RAY DIFFRACTION7A81 - 90
8X-RAY DIFFRACTION8A91 - 110
9X-RAY DIFFRACTION9A111 - 128
10X-RAY DIFFRACTION10A129 - 135
11X-RAY DIFFRACTION11A136 - 153
12X-RAY DIFFRACTION12A154 - 159

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