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

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Basic information

Entry
Database: PDB / ID: 4oad
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 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: 1.45 Å
AuthorsMajorek, K.A. / Niedzialkowska, E. / 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 in complex with chloramphenicol
Authors: Majorek, K.A. / Niedzialkowska, E. / 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

Downloads & links

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Assembly

Deposited unit
A: GNAT superfamily acetyltransferase PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,52815
Polymers18,0011
Non-polymers1,52714
Water3,909217
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)39,05530
Polymers36,0012
Non-polymers3,05428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7990 Å2
ΔGint-105 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.754, 76.072, 39.483
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-436-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CLM / 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


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


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
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: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2013 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 31335 / Num. obs: 31335 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 46.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1539 / Rsym value: 0.716 / % 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: 1.45→46 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17924 1583 5.1 %RANDOM
Rwork0.1536 ---
all0.15496 29702 --
obs0.15496 29702 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å20 Å2
2---0.35 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.45→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 92 217 1550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191456
X-RAY DIFFRACTIONr_bond_other_d00.021383
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.971980
X-RAY DIFFRACTIONr_angle_other_deg3.54333163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34322.75469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17115228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9321515
X-RAY DIFFRACTIONr_chiral_restr0.1170.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211685
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02368
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_it1.2821.372681
X-RAY DIFFRACTIONr_mcbond_other1.2521.369680
X-RAY DIFFRACTIONr_mcangle_it1.9052.059864
X-RAY DIFFRACTIONr_mcangle_other1.9052.062865
X-RAY DIFFRACTIONr_scbond_it2.6151.856775
X-RAY DIFFRACTIONr_scbond_other2.6061.856775
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8582.6411109
X-RAY DIFFRACTIONr_long_range_B_refined7.18414.2481733
X-RAY DIFFRACTIONr_long_range_B_other6.72112.8431629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 97 -
Rwork0.264 1990 -
obs-1990 90.62 %
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)
10.7302-0.65840.14231.63890.03121.09960.00980.01340.0037-0.022-0.0144-0.03830.01770.03380.00450.05720.00490.00440.07820.00960.013114.50915.2991.454
20.6734-0.01860.74221.18691.24212.20910.0656-0.1007-0.02580.0772-0.0266-0.00810.1978-0.1994-0.0390.1018-0.01660.00510.12260.0180.02447.10710.1611.13
30.3954-0.16560.14751.1797-1.14892.6378-0.0401-0.05380.0261-0.016-0.0213-0.07720.0662-0.04360.06140.05870.0163-0.00170.0823-0.00420.01113.20215.88711.747
41.16980.1913-0.54181.0017-0.33512.3759-0.0340.01750.06670.04630.0092-0.0779-0.09620.03010.02470.0620.0112-0.01060.06060.00670.013320.76719.0869.552
51.0209-0.3584-0.93840.71550.68441.19090.0438-0.0090.0852-0.01220.0179-0.006-0.0929-0.0776-0.06170.09450.0275-0.00230.08550.00160.010922.2929.96515.81
61.57490.98922.51822.47392.57725.830.0177-0.0601-0.05640.0218-0.00130.08990.1259-0.1452-0.01650.05490.00210.00040.04610.00310.013121.353-3.9288.182
74.9688-1.5118-3.03766.02832.0734.65480.0594-0.28750.14320.0843-0.0128-0.0694-0.25160.1396-0.04670.08780.0178-0.00580.0928-0.00820.005223.26410.93521.883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 34
2X-RAY DIFFRACTION2A35 - 49
3X-RAY DIFFRACTION3A50 - 81
4X-RAY DIFFRACTION4A82 - 105
5X-RAY DIFFRACTION5A106 - 134
6X-RAY DIFFRACTION6A135 - 153
7X-RAY DIFFRACTION7A154 - 159

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