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

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Basic information

Entry
Database: PDB / ID: 4kou
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with Cefixime
ComponentsUncharacterized protein
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acetyltransferase activity / 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
Chem-C04 / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMajorek, K.A. / Chruszcz, M. / Otwinowski, Z. / 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 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Apr 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 1.5Sep 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,57411
Polymers18,0011
Non-polymers1,57310
Water3,855214
1


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

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,14822
Polymers36,0012
Non-polymers3,14720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4250 Å2
ΔGint-109 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.709, 75.998, 39.435
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


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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-C04 / (6R,7R)-7-({(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetyl}amino)-3-ethenyl-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid / Cefixime


Mass: 453.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N5O7S2 / Comment: medication, antibiotic*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 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: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2010 / Details: Beryllium Lenses
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 23767 / Num. obs: 23767 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 39.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1180 / Rsym value: 0.685 / % possible all: 100

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Processing

Software
NameVersionClassification
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: 1.6→29.95 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19103 1200 5.1 %RANDOM
Rwork0.15794 ---
all0.15962 22360 --
obs0.15962 22360 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---1.55 Å2-0 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 97 214 1546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021472
X-RAY DIFFRACTIONr_bond_other_d00.021345
X-RAY DIFFRACTIONr_angle_refined_deg21.9812013
X-RAY DIFFRACTIONr_angle_other_deg3.7193.0083066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00522.98567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50615215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.211513
X-RAY DIFFRACTIONr_chiral_restr0.1560.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211672
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02362
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 86 -
Rwork0.233 1623 -
obs-1623 100 %
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)
113.7349-3.7342-14.307410.2351.726125.9730.3001-0.63721.0601-0.3569-0.1364-1.2933-1.32071.7969-0.16370.2436-0.0477-0.05320.2120.03440.251320.19728.458.637
20.873-0.38260.31081.6038-0.13771.46950.01950.0325-0.0286-0.0841-0.0152-0.03040.0669-0.0365-0.00420.13620.014-0.00010.12420.01190.009811.58214.3611.87
30.8274-0.2331-0.18591.362-0.40546.29880.0234-0.0948-0.04320.02920.05490.02620.203-0.1748-0.07820.14810.01180.00630.13660.00880.004311.5549.66818.247
45.11430.34410.94162.8108-0.01014.8817-0.06150.3583-0.033-0.16520.0098-0.1302-0.01560.20990.05170.1310.00970.020.13340.01490.033223.27618.6831.664
54.1381.0941-1.45683.9484-1.84384.5309-0.03490.1120.10180.03630.0085-0.1572-0.11670.04020.02630.17340.0221-0.01880.1201-0.0030.022919.50219.59714.991
613.76262.69090.272513.4937-0.16714.90040.14450.30780.5773-0.16510.01820.3854-0.7120.0115-0.16270.18510.04190.02140.1152-0.00740.037811.98417.62423.656
70.7748-0.5448-0.6270.8290.4640.65330.0121-0.0440.01950.05020.0039-0.0765-0.0465-0.0966-0.01610.14310.0107-0.00550.1259-0.00050.009523.1317.1612.965
81.07141.38710.47128.67380.1092.0873-0.0463-0.02260.06060.21080.0416-0.3588-0.09580.0230.00460.15650.018-0.01020.1486-0.00760.03427.1787.07916.689
91.08660.58551.00772.25431.5973.2804-0.0202-0.105-0.0303-0.0393-0.03350.1192-0.0388-0.13260.05360.14220.0058-0.0020.13190.00520.025720.651-0.8769.742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 66
3X-RAY DIFFRACTION3A67 - 81
4X-RAY DIFFRACTION4A82 - 93
5X-RAY DIFFRACTION5A94 - 103
6X-RAY DIFFRACTION6A104 - 109
7X-RAY DIFFRACTION7A110 - 127
8X-RAY DIFFRACTION8A128 - 138
9X-RAY DIFFRACTION9A139 - 159

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