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- PDB-3pgp: Crystal structure of PA4794 - GNAT superfamily protein in complex... -

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Basic information

Entry
Database: PDB / ID: 3pgp
TitleCrystal structure of PA4794 - GNAT superfamily protein in complex with AcCoA
Componentsuncharacterized protein PA4794
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / acetyltransferase / GNAT family / PSI
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
ACETYL COENZYME *A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 26, 2012Group: Structure summary
Revision 1.3Dec 19, 2012Group: Structure summary
Revision 1.4Jun 5, 2013Group: Other
Revision 1.5Sep 18, 2013Group: Database references
Revision 1.6May 7, 2014Group: Database references
Revision 1.7Apr 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 1.8Sep 6, 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

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Assembly

Deposited unit
A: uncharacterized protein PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,28010
Polymers18,0011
Non-polymers1,2809
Water4,089227
1


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

A: uncharacterized protein PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,56020
Polymers36,0012
Non-polymers2,55918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6690 Å2
ΔGint-14 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.673, 76.286, 39.311
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 uncharacterized protein 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 48.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 M Ammonium Sulfate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 13, 2009 / 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: 1.42→50 Å / Num. all: 32584 / Num. obs: 32584 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.321 / Net I/σ(I): 58.6
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1633 / Rsym value: 0.321 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i6c

2i6c
PDB Unreleased entry


Resolution: 1.42→46.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.841 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20219 1634 5.1 %RANDOM
Rwork0.17229 ---
all0.17383 30700 --
obs0.17383 30700 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.272 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--0.36 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.42→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 80 227 1537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221407
X-RAY DIFFRACTIONr_bond_other_d0.0060.02960
X-RAY DIFFRACTIONr_angle_refined_deg2.012.0051909
X-RAY DIFFRACTIONr_angle_other_deg1.00432315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62822.78761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33715212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2941512
X-RAY DIFFRACTIONr_chiral_restr0.1260.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
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_it1.1731.5843
X-RAY DIFFRACTIONr_mcbond_other0.4191.5339
X-RAY DIFFRACTIONr_mcangle_it1.85421344
X-RAY DIFFRACTIONr_scbond_it2.8143564
X-RAY DIFFRACTIONr_scangle_it4.1774.5565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 108 -
Rwork0.289 2335 -
obs--99.19 %
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)
10.6827-0.49380.55760.7868-0.23551.22630.02360.00040.1037-0.0839-0.0359-0.06820.0142-0.02440.01230.12130.01310.00660.02620.0060.029-15.80213.51-19.093
21.07470.00670.37051.039-0.37121.7851-0.0482-0.08740.13720.05170.0349-0.0233-0.0502-0.08040.01330.11190.02870.0060.0211-0.01120.0236-13.31816.516-8.84
30.4022-0.24130.061.39510.29740.7485-0.0192-0.0824-0.02630.08570.02030.0619-0.018-0.1128-0.00110.12920.01950.00410.0335-0.00010.0266-7.534.847-6.493
41.8833-1.9695-0.66585.50021.80382.4337-0.0866-0.28190.11440.29520.1478-0.2258-0.060.1135-0.06120.18610.0341-0.01660.0951-0.01620.0381-5.8289.0241.751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1001 - 1045
2X-RAY DIFFRACTION2A1046 - 1104
3X-RAY DIFFRACTION3A1105 - 1151
4X-RAY DIFFRACTION4A1152 - 1160

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