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

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Basic information

Entry
Database: PDB / ID: 4oae
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 C29A/C117A/Y128A mutant in complex with chloramphenicol
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
CHLORAMPHENICOL / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMajorek, K.A. / Chruszcz, M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a GNAT superfamily acetyltransferase PA4794 C29A/C117A/Y128A mutant in complex with chloramphenicol
Authors: Majorek, K.A. / Chruszcz, M. / Joachimiak, A. / Minor, W.
History
DepositionJan 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Apr 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 1.3Sep 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

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Assembly

Deposited unit
A: GNAT superfamily acetyltransferase PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,56417
Polymers17,8441
Non-polymers1,71916
Water4,360242
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)39,12734
Polymers35,6892
Non-polymers3,43832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8240 Å2
ΔGint-139 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.880, 75.626, 39.482
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: 17844.375 Da / Num. of mol.: 1 / Mutation: C29A, C117A, Y128A
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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol


Mass: 323.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 49.2 %
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: 0.91837 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2012 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 48658 / Num. obs: 48658 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 43.7
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2440 / Rsym value: 0.747 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
DENZO3000: MOLREPdata reduction
SCALEPACK3000: MOLREPdata scaling
REFMAC5.8.0049refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KUA

4kua


Resolution: 1.25→45.96 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15476 2456 5.1 %RANDOM
Rwork0.12037 ---
all0.1221 46151 --
obs0.1221 46151 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å20 Å2
2---0.85 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.25→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 102 242 1583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191492
X-RAY DIFFRACTIONr_bond_other_d00.021428
X-RAY DIFFRACTIONr_angle_refined_deg1.921.9782027
X-RAY DIFFRACTIONr_angle_other_deg3.50433272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.322.77872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08815238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6151516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211706
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02372
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_it1.7731.377682
X-RAY DIFFRACTIONr_mcbond_other1.66146.667681
X-RAY DIFFRACTIONr_mcangle_it1.972.07863
X-RAY DIFFRACTIONr_mcangle_other1.978864
X-RAY DIFFRACTIONr_scbond_it4.5961.98810
X-RAY DIFFRACTIONr_scbond_other4.59925.178810
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8181151
X-RAY DIFFRACTIONr_long_range_B_refined5.3311815
X-RAY DIFFRACTIONr_long_range_B_other5.3341816
X-RAY DIFFRACTIONr_rigid_bond_restr8.64531488
X-RAY DIFFRACTIONr_sphericity_free42.413561
X-RAY DIFFRACTIONr_sphericity_bonded17.32251625
LS refinement shellResolution: 1.251→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 179 -
Rwork0.197 3359 -
obs-3359 99.72 %

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