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

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Basic information

Entry
Database: PDB / ID: 4kov
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with Cefuroxime
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-KOV / 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 1.3Apr 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

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,21013
Polymers18,0011
Non-polymers1,20912
Water2,900161
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)38,41926
Polymers36,0012
Non-polymers2,41824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5620 Å2
ΔGint-49 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.621, 76.472, 39.473
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-KOV / (6R,7R)-3-[(carbamoyloxy)methyl]-7-{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid / Cefuroxime


Mass: 424.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4O8S
#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.: 161 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
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-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 13, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 24348 / Num. obs: 24348 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 42.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1198 / Rsym value: 0.66 / % possible all: 99.8

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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: 1.6→27.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.311 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19302 1227 5.1 %RANDOM
Rwork0.1624 ---
all0.16396 22861 --
obs0.16396 22861 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.43 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 76 161 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191431
X-RAY DIFFRACTIONr_bond_other_d0.0030.021365
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.9821936
X-RAY DIFFRACTIONr_angle_other_deg0.9233118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8622.68767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46415220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9571514
X-RAY DIFFRACTIONr_chiral_restr0.120.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
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
Rfree0.275 109 -
Rwork0.25 1637 -
obs-1637 99.89 %
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)
11.0463-1.42290.66123.8694-1.07833.02790.11280.10510.104-0.3204-0.1869-0.13090.12170.13450.07410.25050.02980.0240.1160.02450.031314.58514.9241.266
21.099-0.36950.77951.6484-0.33272.57260.010.01230.0792-0.0840.0361-0.00840.1481-0.1311-0.04610.23620.03220.01370.09290.01270.01312.36714.0187.816
34.84491.3136-3.53813.5894-2.45236.17390.05950.01590.30980.31240.07240.039-0.293-0.1246-0.1320.27880.0383-0.00930.077-0.00010.026318.10719.25516.41
41.6112-0.9401-0.72242.11271.64311.70490.0735-0.02780.1284-0.01750.0903-0.2231-0.1536-0.0598-0.16390.27570.0314-0.00140.07920.00240.030425.0926.87814.337
51.34750.16350.56113.47072.5733.9234-0.0105-0.1149-0.1229-0.08120.13150.0194-0.1387-0.0847-0.12090.29820.0159-0.00970.11380.01580.05421.3060.61810.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 33
2X-RAY DIFFRACTION2A34 - 88
3X-RAY DIFFRACTION3A89 - 109
4X-RAY DIFFRACTION4A110 - 139
5X-RAY DIFFRACTION5A140 - 159

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