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- PDB-3ijw: Crystal structure of BA2930 in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 3ijw
TitleCrystal structure of BA2930 in complex with CoA
ComponentsAminoglycoside N3-acetyltransferase
KeywordsTRANSFERASE / anthrax / CoA / Acyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyaminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / ACETYL COENZYME *A / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKlimecka, M.M. / Chruszcz, M. / Skarina, T. / Onopryienko, O. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis.
Authors: Klimecka, M.M. / Chruszcz, M. / Font, J. / Skarina, T. / Shumilin, I. / Onopryienko, O. / Porebski, P.J. / Cymborowski, M. / Zimmerman, M.D. / Hasseman, J. / Glomski, I.J. / Lebioda, L. / ...Authors: Klimecka, M.M. / Chruszcz, M. / Font, J. / Skarina, T. / Shumilin, I. / Onopryienko, O. / Porebski, P.J. / Cymborowski, M. / Zimmerman, M.D. / Hasseman, J. / Glomski, I.J. / Lebioda, L. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside N3-acetyltransferase
B: Aminoglycoside N3-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4248
Polymers60,6742
Non-polymers1,7506
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-30 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.854, 109.957, 133.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein Aminoglycoside N3-acetyltransferase


Mass: 30337.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: AMES / Gene: aacC7, BA_2930, GBAA2930, GBAA_2930 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) / References: UniProt: Q81P86, UniProt: A0A3P1UCA6*PLUS
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M MgCl2, 15% w/v PEG3350, 10 mM butyryl-CoA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 11, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→34.6 Å / Num. all: 44002 / Num. obs: 44002 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 28.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2173 / Rsym value: 0.555 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0072refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E4F

3e4f


Resolution: 1.9→34.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.476 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23065 2203 5 %RANDOM
Rwork0.18567 ---
all0.18791 41511 --
obs0.18791 41511 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 100 336 4551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224332
X-RAY DIFFRACTIONr_bond_other_d00.022905
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9785899
X-RAY DIFFRACTIONr_angle_other_deg4.18837104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44224.157178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.415732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.411526
X-RAY DIFFRACTIONr_chiral_restr0.1220.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214745
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02845
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_it0.9771.52645
X-RAY DIFFRACTIONr_mcbond_other01.51078
X-RAY DIFFRACTIONr_mcangle_it1.74324303
X-RAY DIFFRACTIONr_scbond_it3.08431687
X-RAY DIFFRACTIONr_scangle_it4.6434.51596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3401 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.485
loose thermal2.9610
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 152 -
Rwork0.269 3010 -
obs--99.28 %
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)
10.190.1628-0.03352.1302-1.1171.44460.0529-0.0499-0.0744-0.0223-0.1321-0.12420.20940.07130.07910.1227-0.0128-0.00920.10960.02890.032711.71-0.5069.936
20.48060.21720.31820.8138-0.77572.03750.0449-0.044-0.19290.056-0.1182-0.16320.20450.2080.07320.1751-0.0102-0.02160.1360.04370.118512.333-1.7468.812
30.32710.1648-0.13510.5431-0.42381.44070.0168-0.0655-0.10840.0205-0.0067-0.03950.1369-0.0073-0.01010.0793-0.0017-0.01370.09610.00130.04410.727-0.0368.321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 65
2X-RAY DIFFRACTION1B1 - 73
3X-RAY DIFFRACTION2A66 - 110
4X-RAY DIFFRACTION2B74 - 127
5X-RAY DIFFRACTION3A111 - 264
6X-RAY DIFFRACTION3B128 - 264

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