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- PDB-4lua: Crystal structure of N-acetyltransferase from Staphylococcus aure... -

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Basic information

Entry
Database: PDB / ID: 4lua
TitleCrystal structure of N-acetyltransferase from Staphylococcus aureus Mu50
ComponentsN-acetyltransferase
KeywordsTRANSFERASE / NAT_SF / acetyltransferase
Function / homology
Function and homology information


N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) domain / 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
N-acetyltransferase domain-containing protein / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6001 Å
AuthorsSrivastava, P. / Forwood, J.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Purification, crystallization and preliminary X-ray diffraction analysis of the N-acetyltransferase SAV0826 from Staphylococcus aureus.
Authors: Srivastava, P. / Khandokar, Y.B. / Forwood, J.K.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3452
Polymers19,2531
Non-polymers921
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.939, 84.939, 49.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

#1: Protein N-acetyltransferase


Mass: 19252.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV0826 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q99VI0, UniProt: A0A0H3JYD9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.25M sodium formate,100mM sodium acetate trihydrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→28.31 Å / Num. all: 24260 / Num. obs: 24239 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 5.2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
Blu-Ice(McPhillipsdata collection
CCP4model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G8W

3g8w


Resolution: 1.6001→26.86 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 1235 5.11 %
Rwork0.1784 --
obs0.1798 24191 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6001→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 6 154 1436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191327
X-RAY DIFFRACTIONf_angle_d1.7541797
X-RAY DIFFRACTIONf_dihedral_angle_d14.661486
X-RAY DIFFRACTIONf_chiral_restr0.133205
X-RAY DIFFRACTIONf_plane_restr0.008228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.66410.27711120.22952483X-RAY DIFFRACTION98
1.6641-1.73980.25611380.20792492X-RAY DIFFRACTION100
1.7398-1.83160.24691680.19162479X-RAY DIFFRACTION100
1.8316-1.94630.18651340.18722516X-RAY DIFFRACTION100
1.9463-2.09650.20791270.17642548X-RAY DIFFRACTION100
2.0965-2.30740.2371510.17532523X-RAY DIFFRACTION100
2.3074-2.6410.21351370.18342574X-RAY DIFFRACTION100
2.641-3.32640.18611350.17962595X-RAY DIFFRACTION100
3.3264-26.8640.19511330.16612746X-RAY DIFFRACTION100
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)
10.31590.1663-0.03530.2541-0.33440.49830.0145-0.2482-0.16320.05840.0373-0.3112-0.5844-0.03570.02780.2549-0.01380.01330.1615-0.02080.1721-27.7369.82856.4994
20.4349-0.34180.18170.7953-0.5150.71710.2169-0.11980.04310.69230.3338-0.6075-0.44330.15660.55750.3701-0.0944-0.06740.2586-0.13840.2747-18.86036.778616.2935
30.62250.1479-0.06950.0416-0.10040.1348-0.3584-0.50470.09770.3824-0.0602-0.6403-0.44020.1976-0.22790.2607-0.0327-0.12080.25420.03410.2329-21.4393-8.316917.6204
40.76380.0785-0.09990.3928-0.31971.99490.3054-0.10260.43930.21490.1004-0.9028-0.57320.48930.48010.1882-0.0777-0.07740.2096-0.10270.4278-18.14835.65569.1047
50.6017-0.058-0.18050.5205-0.37371.03090.0167-0.1581-0.215-0.3096-0.0667-0.227-0.57520.3485-0.06810.2023-0.04490.01680.1475-0.01160.2132-21.31880.69626.4849
60.0638-0.00120.0344-0.0043-0.00350.0065-0.07960.2861-0.0768-0.38390.1452-0.92730.3310.65240.00850.24040.04320.13090.3483-0.04350.3935-14.9121-7.3932-2.5248
70.4174-0.1434-0.18920.9990.31940.13270.08050.0002-0.0229-0.1388-0.07520.1026-0.1423-0.05460.00010.17410.0108-0.02780.1255-0.01590.1565-29.2045-0.83185.0345
80.4568-0.1290.08181.00760.69260.4247-0.01220.1222-0.1299-0.2106-0.10870.0296-0.0065-0.0138-0.00190.1496-0.0011-0.01480.14040.00840.1262-27.2759-10.59463.0056
9-0.01350.046-0.00310.20380.17670.26740.14580.1011-0.3479-0.2098-0.1850.1347-0.0170.30420.00350.11420.0314-0.03070.1602-0.00170.1661-25.655-17.86361.4322
100.62450.5831-0.51261.118-0.51880.39680.4584-0.107-0.28940.9256-0.1956-0.50880.48760.44030.13970.29640.0068-0.10380.27490.05940.2724-15.708-18.453615.3209
111.36780.1351-0.04580.1340.07940.0631-0.06040.2713-0.2167-0.58660.0349-0.10550.12360.0504-0.21120.2898-0.0069-0.01410.1641-0.02060.1109-25.6187-13.0588-2.5962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 37 )
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 84 )
7X-RAY DIFFRACTION7chain 'A' and (resid 85 through 109 )
8X-RAY DIFFRACTION8chain 'A' and (resid 110 through 133 )
9X-RAY DIFFRACTION9chain 'A' and (resid 134 through 141 )
10X-RAY DIFFRACTION10chain 'A' and (resid 142 through 153 )
11X-RAY DIFFRACTION11chain 'A' and (resid 154 through 163 )

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