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- PDB-1bo4: CRYSTAL STRUCTURE OF A GCN5-RELATED N-ACETYLTRANSFERASE: SERRATIA... -

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Basic information

Entry
Database: PDB / ID: 1bo4
TitleCRYSTAL STRUCTURE OF A GCN5-RELATED N-ACETYLTRANSFERASE: SERRATIA MARESCENS AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE
ComponentsPROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)
KeywordsTRANSFERASE / AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE / EUBACTERIAL AMINOGLYCOSIDE RESISTANCE / GCN5-RELATED N-ACETYLTRANSFERASE / COA-BINDING
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
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
COENZYME A / SPERMIDINE / Aminoglycoside-(3)-N-acetyltransferase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWolf, E. / Vassilev, A. / Makino, Y. / Sali, A. / Nakatani, Y. / Burley, S.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase.
Authors: Wolf, E. / Vassilev, A. / Makino, Y. / Sali, A. / Nakatani, Y. / Burley, S.K.
History
DepositionAug 8, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)
B: PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6565
Polymers36,9762
Non-polymers1,6803
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-17 kcal/mol
Surface area13600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.540, 102.260, 50.140
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999954, 9.4E-5, 0.009258), (-3.2E-5, -0.999973, 0.007015), (0.009257, 0.007011, 0.999933)
Vector: 32.1835, 126.8667, -0.6064)

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Components

#1: Protein PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)


Mass: 18487.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Cell: EUBACTERIA / Cellular location: CYTOPLASM / Gene: AACC1 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53396
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: SITTING DROP, 4 DEGREES C, 3.5MG/ML PROTEIN + 5MM COA, 100MM TRIS-HCL PH7.8, 0.8% PEG4K, 18% T-BUTANOL, 20MM SRCL2, 7% DIOXANE, 5% 2,4-METHYLPENTANEDIOL, 40MM HEXANEDIOL, 10MM ...Details: SITTING DROP, 4 DEGREES C, 3.5MG/ML PROTEIN + 5MM COA, 100MM TRIS-HCL PH7.8, 0.8% PEG4K, 18% T-BUTANOL, 20MM SRCL2, 7% DIOXANE, 5% 2,4-METHYLPENTANEDIOL, 40MM HEXANEDIOL, 10MM DITHIOTHREITOL, 2MM TRIS(2-CARBOXY- ETHYL)PHOSPHINE-HCL, 10MM SPERMIDINE, 2.5% GLYCEROL, vapor diffusion - sitting drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 mg/mlprotein1drop
25 mMCoA1drop
3100 mMTris-HCl1reservoir
40.8 %PEG40001reservoir
518 %t-butanol1reservoir
620 mM1reservoirSrCl2
77 %dioxane1reservoir
850 %MPD1reservoir
940 mMhexanediol1reservoir
1010 mMdithiothreitol1reservoir
112 mMtri(2-carboxyethyl)phosphine-HCl1reservoir
1210 mMspermidine1reservoir
132.5 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9793, 0.9703, 0.9668
DetectorDetector: CCD / Date: May 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97031
30.96681
ReflectionResolution: 2.3→20 Å / Num. obs: 16291 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.052 / Net I/σ(I): 7.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.093 / % possible all: 92.9
Reflection
*PLUS
Num. measured all: 118408 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 92.9 % / Rmerge(I) obs: 0.093

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.3Crefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→15 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -10 %RANDOM
Rwork0.201 ---
obs0.201 15675 89.5 %-
Solvent computationBsol: 49.7 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.276 Å20 Å2-4.699 Å2
2--3.986 Å20 Å2
3----5.262 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 106 253 2475
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.7792
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.5982.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.33 Å / Total num. of bins used: 31
RfactorNum. reflection% reflection
Rfree0.232 -10 %
Rwork0.193 424 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3COA_2.PARCOA_2.TOP
X-RAY DIFFRACTION4SPD.PARSPD.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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