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- PDB-4m85: Crystal structure of N-acetyltransferase from Staphylococcus aure... -

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Basic information

Entry
Database: PDB / ID: 4m85
TitleCrystal structure of N-acetyltransferase from Staphylococcus aureus Mu50
ComponentsN-acetyltransferase
KeywordsTRANSFERASE / GNAT fold / acetyltransferase
Function / homology
Function and homology information


N-acetyltransferase activity
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
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: 2 Å
AuthorsSrivastava, P. / Khandokar, Y. / Forwood, J.K.
CitationJournal: To be Published
Title: Expression,purification and X-ray crystallography of N-acetyltransferase from Staphylococcus aureus
Authors: Srivastava, P. / Khandokar, Y. / Forwood, J.K.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyltransferase
B: N-acetyltransferase
C: N-acetyltransferase
D: N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)86,6364
Polymers86,6364
Non-polymers00
Water9,494527
1
A: N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)21,6591
Polymers21,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)21,6591
Polymers21,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)21,6591
Polymers21,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)21,6591
Polymers21,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.460, 68.970, 73.460
Angle α, β, γ (deg.)67.23, 91.69, 75.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
N-acetyltransferase /


Mass: 21658.879 Da / Num. of mol.: 4 / Fragment: enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV1040 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q99V53, UniProt: A0A0H3JUR0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 22%PEG8000,50mM Potassium phosphate monobasic, 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: 2→36.28 Å / Num. all: 53259 / Num. obs: 49478 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
Blu-Ice(McPhillipsdata collection
CCP4model building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1U6M

1u6m


Resolution: 2→36.28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.949 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23912 2495 5 %RANDOM
Rwork0.1917 ---
obs0.19409 46952 92.87 %-
all-50594 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.369 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20.01 Å2-0.04 Å2
2---0.04 Å20.07 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6018 0 0 527 6545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196150
X-RAY DIFFRACTIONr_bond_other_d0.0010.025900
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9668322
X-RAY DIFFRACTIONr_angle_other_deg0.756313620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7424.759290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.404151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5651524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021347
X-RAY DIFFRACTIONr_mcbond_it1.5842.622936
X-RAY DIFFRACTIONr_mcbond_other1.5822.622935
X-RAY DIFFRACTIONr_mcangle_it2.4953.9233663
X-RAY DIFFRACTIONr_mcangle_other2.4953.9243664
X-RAY DIFFRACTIONr_scbond_it2.2422.9293214
X-RAY DIFFRACTIONr_scbond_other2.2412.9293215
X-RAY DIFFRACTIONr_scangle_other3.5484.2724660
X-RAY DIFFRACTIONr_long_range_B_refined5.69122.1567667
X-RAY DIFFRACTIONr_long_range_B_other5.45221.7447445
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 187 -
Rwork0.284 3433 -
obs--92.04 %

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