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- PDB-4zbg: Crystal Structure of a GNAT family Acetyltransferase from Brucell... -

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Basic information

Entry
Database: PDB / ID: 4zbg
TitleCrystal Structure of a GNAT family Acetyltransferase from Brucella melitensis in complex with Acetyl-CoA
ComponentsAcetyltransferase
KeywordsTRANSFERASE / SGCID / N-acetyltransferase / Acyl_CoA_acyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
ACETYL COENZYME *A / Acetyltransferase
Similarity search - Component
Biological speciesBrucella abortus str. 2308 A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a GNAT family Acetyltransferase from Brucella melitensis in complex with Acetyl-CoA
Authors: SSGCID / Dranow, D.M. / Trakaki, T. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list ...entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / reflns_shell
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5333
Polymers18,6311
Non-polymers9022
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.810, 57.110, 44.060
Angle α, β, γ (deg.)90.000, 96.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acetyltransferase


Mass: 18631.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus str. 2308 A (bacteria)
Strain: 2308 A / Gene: BAAA_2000484 / Plasmid: BrabA.17468.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4IR59
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 241 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BrabA.17468.b.B1.PS02320 at 10.4mg/ml, mixed with 4mM acetyl-CoA, then 1:1 with MCSG1(c12): 0.1M Bis-Tris:HCl, pH=6.5, 25% PEG-3350, cryo-protected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionNumber: 218334 / Rmerge(I) obs: 0.04 / Χ2: 0.99 / D res high: 1.25 Å / Num. obs: 40267 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
3.955.5985810.025
3.233.95108810.025
2.83.23128010.028
2.52.8144610.031
2.282.5161010.032
2.112.28173310.033
1.982.11189810.037
1.861.98195710.039
1.771.86211310.048
1.691.77221010.055
1.611.69231310.066
1.551.61240010.078
1.491.55248210.091
1.441.49259110.111
1.41.44267210.137
1.361.4274310.169
1.321.36287310.203
1.281.32286410.238
1.251.28268210.26
ReflectionResolution: 1.25→50 Å / Num. obs: 40267 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 9.23 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.045 / Χ2: 0.991 / Net I/σ(I): 23.66 / Num. measured all: 218334
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.25-1.2840.9320.264.8210635295426820.390.8
1.28-1.320.9580.2386.3214220290928640.26798.5
1.32-1.360.970.2037.8115682287628730.22599.9
1.36-1.40.9810.1699.4115101274027430.188100
1.4-1.440.9860.13711.3514701267326720.152100
1.44-1.490.9910.11113.7514326259225910.122100
1.49-1.550.9940.09116.5213803248224820.1100
1.55-1.610.9960.07819.1513368240224000.08699.9
1.61-1.690.9960.06622.1912935231423130.073100
1.69-1.770.9970.05525.7912392220922100.061100
1.77-1.860.9980.04828.9111882211621130.05299.9
1.86-1.980.9990.03935.3711071195319570.043100
1.98-2.110.9990.03738.8210718189818980.04100
2.11-2.280.9990.03342.539814173317330.037100
2.28-2.50.9990.03244.839071161416100.03599.8
2.5-2.80.9990.03147.598204144514460.034100
2.8-3.230.9990.02850.867234128312800.03199.8
3.23-3.950.9990.02553.836136108910880.02899.9
3.95-5.590.9990.02554.4647398598580.02899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RS2

4rs2


Resolution: 1.25→26.291 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.163 2003 4.98 %
Rwork0.1417 38238 -
obs0.1429 40241 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.45 Å2 / Biso mean: 15.191 Å2 / Biso min: 4.7 Å2
Refinement stepCycle: final / Resolution: 1.25→26.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 57 247 1466
Biso mean--16.16 26.29 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061324
X-RAY DIFFRACTIONf_angle_d1.2041803
X-RAY DIFFRACTIONf_chiral_restr0.068183
X-RAY DIFFRACTIONf_plane_restr0.005236
X-RAY DIFFRACTIONf_dihedral_angle_d17.096498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.28120.22411280.1592451257991
1.2812-1.31590.17261480.14362699284798
1.3159-1.35460.17231300.136827772907100
1.3546-1.39830.19221250.130227592884100
1.3983-1.44830.17951450.12827062851100
1.4483-1.50630.15281460.121727742920100
1.5063-1.57480.15231420.123527642906100
1.5748-1.65780.161310.127827522883100
1.6578-1.76170.15791430.130527632906100
1.7617-1.89770.16821380.138727602898100
1.8977-2.08860.17421670.133427162883100
2.0886-2.39060.15961390.14727752914100
2.3906-3.01120.16031460.157327772923100
3.0112-26.29720.15351750.14982765294099

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