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

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Basic information

Entry
Database: PDB / ID: 4kow
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with Cefoxitin
ComponentsUncharacterized protein
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
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
CEFOXITIN / 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. / Porebski, P.J. / Chruszcz, M. / Grabowski, 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
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)19,64720
Polymers18,0011
Non-polymers1,64719
Water3,441191
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)39,29540
Polymers36,0012
Non-polymers3,29338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area9940 Å2
ΔGint-21 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.851, 76.444, 39.444
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-423-

HOH

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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-CFX / CEFOXITIN


Mass: 427.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O7S2 / Comment: antibiotic*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 49.23 %
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: 1.45→50 Å / Num. all: 31590 / Num. obs: 31590 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 49.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1561 / Rsym value: 0.634 / % possible all: 100

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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: 1.45→27.07 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15835 1590 5 %RANDOM
Rwork0.14044 ---
all0.14135 29958 --
obs0.14135 29958 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0 Å2
2---0.39 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 103 191 1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191473
X-RAY DIFFRACTIONr_bond_other_d00.021420
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.9921984
X-RAY DIFFRACTIONr_angle_other_deg3.58533242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96122.38867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87415227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8041515
X-RAY DIFFRACTIONr_chiral_restr0.1130.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211687
X-RAY DIFFRACTIONr_gen_planes_other0.020.02362
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: 1.452→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 103 -
Rwork0.261 2173 -
obs-2173 98.83 %
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)
16.0631-0.681.27124.98530.22235.9119-0.2256-0.0570.28530.06480.09090.5214-0.4304-0.31530.13480.14-0.017-0.00690.0432-0.00550.1229-16.03626.785-8.604
23.80693.0549-1.01524.039-1.43962.63610.0865-0.20.02590.116-0.1211-0.0702-0.14380.15880.03450.0685-0.01760.00530.0494-0.01410.0224-9.79119.1641.333
33.3617-0.0103-0.97573.13011.22215.81280.0116-0.1431-0.040.2372-0.0216-0.01090.3544-0.04470.00990.0872-0.026-0.00970.04290.00350.008-16.1975.350.915
41.44970.4519-0.03511.455-0.76923.98230.0472-0.0520.01690.0596-0.0043-0.0530.18370.3763-0.04280.0584-0.001-0.00730.076-0.01570.0132-7.05110.37-0.828
51.2529-0.06180.23323.5391.51563.0707-0.00930.00950.1436-0.0182-0.00260.0572-0.11330.04070.0120.0578-0.02920.00040.05240.00220.0445-13.35818.44-8.694
60.5871-0.0108-1.17491.31391.056412.1669-0.01360.13560.0222-0.08070.00410.00860.09660.15410.00950.0552-0.01690.00120.05960.00430.0101-13.30510.535-18.083
72.8352-0.43431.17241.1585-0.84653.14-0.0578-0.26150.07890.20360.05550.1728-0.1994-0.20070.00240.0759-0.00140.03150.0543-0.0260.0649-23.45418.92-1.609
85.1659-1.0574-1.9134.87152.64174.8888-0.0503-0.06460.1803-0.0230.02260.1516-0.1409-0.07080.02760.0733-0.0181-0.01420.02120.00890.027-19.76119.765-14.844
926.7146-2.7559-6.547513.13433.505911.72250.580.09680.709-0.3332-0.1874-0.0111-0.9237-0.0239-0.39260.1617-0.05610.03130.06980.00950.0274-13.2918.216-23.304
101.32010.691-0.97331.4305-1.14311.32240.08250.030.11150.08710.02990.1477-0.18530.0566-0.11250.07-0.03110.0010.03630.01080.0205-23.9828.978-14.004
114.8924-1.11612.30925.1137-2.0054.29930.09890.1907-0.1752-0.25230.08620.17310.21810.1375-0.18520.084-0.01790.00170.0374-0.02330.0251-23.465-1.715-15.107
121.8152-1.44072.56323.5661-4.25597.4210.0503-0.0446-0.13650.12540.12070.0040.09860.0314-0.17090.08490.0042-0.01650.0278-0.00470.0318-20.814-3.707-5.328
1310.62065.8867-2.70339.70610.32178.7548-0.14560.75710.5383-0.48220.34880.1806-0.6139-0.1808-0.20310.1203-0.0349-0.00710.09980.04440.0312-22.74212.483-24.042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2A9 - 20
3X-RAY DIFFRACTION3A21 - 34
4X-RAY DIFFRACTION4A35 - 49
5X-RAY DIFFRACTION5A50 - 70
6X-RAY DIFFRACTION6A71 - 81
7X-RAY DIFFRACTION7A82 - 93
8X-RAY DIFFRACTION8A94 - 103
9X-RAY DIFFRACTION9A104 - 108
10X-RAY DIFFRACTION10A109 - 133
11X-RAY DIFFRACTION11A134 - 141
12X-RAY DIFFRACTION12A142 - 154
13X-RAY DIFFRACTION13A155 - 159

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