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- PDB-3slb: Crystal structure of BA2930 in complex with AcCoA and cytosine -

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Basic information

Entry
Database: PDB / ID: 3slb
TitleCrystal structure of BA2930 in complex with AcCoA and cytosine
ComponentsAminoglycoside N3-acetyltransferase
KeywordsTRANSFERASE / ACYLTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


aminoglycoside 3-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic
Similarity search - Function
Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like
Similarity search - Domain/homology
ACETYL COENZYME *A / 6-AMINOPYRIMIDIN-2(1H)-ONE / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside N(3)-acetyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsKlimecka, M.M. / Chruszcz, M. / Porebski, P.J. / Cymborowski, M. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of BA2930 in complex with AcCoA and cytosine
Authors: Klimecka, M.M. / Chruszcz, M. / Porebski, P.J. / Cymborowski, M. / Anderson, W. / Minor, W.
History
DepositionJun 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,65718
Polymers121,0244
Non-polymers4,63314
Water12,070670
1
A: Aminoglycoside N3-acetyltransferase
B: Aminoglycoside N3-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4028
Polymers60,5122
Non-polymers1,8906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-33 kcal/mol
Surface area22640 Å2
MethodPISA
2
D: Aminoglycoside N3-acetyltransferase
C: Aminoglycoside N3-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,25510
Polymers60,5122
Non-polymers2,7438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-35 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.473, 110.630, 73.780
Angle α, β, γ (deg.)90.00, 112.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ADCB

#1: Protein
Aminoglycoside N3-acetyltransferase


Mass: 30256.074 Da / Num. of mol.: 4 / Mutation: H183G
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, aminoglycoside 3-N-acetyltransferase

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Non-polymers , 6 types, 684 molecules

#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5N3O
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 0.18M MgCl2, 15% w/v PEG3350, 2% w/v CHAPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2010 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 70634 / Num. obs: 70634 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3593 / Rsym value: 0.418 / % possible all: 99

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3KZL

3kzl


Resolution: 2→23.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.968 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22957 3546 5 %RANDOM
Rwork0.17431 ---
all0.17712 66906 --
obs0.17712 66906 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.617 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.15 Å2
2---0.14 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→23.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8242 0 297 670 9209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228746
X-RAY DIFFRACTIONr_bond_other_d0.0060.025879
X-RAY DIFFRACTIONr_angle_refined_deg1.481.99111905
X-RAY DIFFRACTIONr_angle_other_deg0.962314375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14951064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46524.23357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.979151463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8881553
X-RAY DIFFRACTIONr_chiral_restr0.0840.21330
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021692
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_it0.6851.55291
X-RAY DIFFRACTIONr_mcbond_other0.1771.52160
X-RAY DIFFRACTIONr_mcangle_it1.27328592
X-RAY DIFFRACTIONr_scbond_it2.36933455
X-RAY DIFFRACTIONr_scangle_it3.5814.53311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 280 -
Rwork0.197 5036 -
obs--98.68 %
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)
11.8919-0.240.1131.4905-0.15540.9355-0.11690.00610.11030.24750.0730.0022-0.14070.04630.04380.1274-0.0108-0.00020.10070.00310.06777.95319.93644.3
21.9976-1.2806-0.63154.48390.12744.38220.22910.3533-0.1727-0.2669-0.09530.2107-0.0558-0.2266-0.13380.03890.002-0.03810.2386-0.02660.1542-1.621-4.44621.854
31.21680.38110.31832.51110.51421.2648-0.1090.0223-0.03970.03720.09970.4751-0.0545-0.17080.00930.019-0.00220.02330.14650.03280.1641-7.9517.91837.356
42.68420.73640.91083.6282-0.1460.5031-0.24380.48290.4273-0.28520.17640.7075-0.22490.07580.06740.24250.007-0.08810.27220.0820.2698-7.15725.49531.265
51.2817-0.34470.54340.4465-0.24291.39710.05990.1345-0.1702-0.03640.00160.15860.0775-0.0072-0.06150.05010.00720.00360.1186-0.00810.092611.432-12.75633.591
63.1696-0.4678-0.92856.7524-3.11875.2616-0.02810.22180.3490.1872-0.3334-0.6707-0.1840.38050.36150.0698-0.057-0.05740.15640.04670.14126.615.35146.294
71.0624-0.21620.24621.65630.12421.2585-0.0359-0.06430.02210.18320.0316-0.0363-0.07430.04320.00430.041-0.00460.00270.07340.0080.015421.677-4.48450.295
83.7952-0.11861.1820.74170.57842.2427-0.02450.36330.1679-0.0657-0.1134-0.14620.06680.41880.1380.0550.03810.01490.18820.05450.13732.151-14.42138.313
91.3180.27440.09391.0006-0.45650.6559-0.0619-0.00160.04210.12770.0346-0.0055-0.04450.06190.02730.0789-0.00620.00730.09530.00190.057221.19620.8488.678
103.5083-0.1037-2.96956.0658-2.07188.48040.12480.2470.0713-0.2771-0.05320.2326-0.0991-0.2613-0.07160.027-0.0164-0.01680.1639-0.03180.083912.694-6.264-11.841
111.13520.3061-0.01691.88680.31020.6487-0.06950.0154-0.0267-0.01690.04940.26450.0453-0.09770.02020.0313-0.01210.00950.12010.00410.08486.1997.8762.794
122.86820.71162.38082.9234-0.06532.2133-0.2480.37730.3489-0.23440.12490.5226-0.14210.21780.12310.1528-0.026-0.07330.21580.06360.19076.36824.903-5.276
130.894-0.19040.37030.5364-0.13941.4383-0.06170.0707-0.12110.01440.03860.08540.0933-0.03150.0230.0471-0.00250.02020.099-0.00720.062626.031-12.6660.902
143.91261.3307-1.90054.3138-1.784.1969-0.07270.04670.1447-0.0505-0.0309-0.321-0.05410.39450.10370.0243-0.023-0.03240.14970.01790.089739.68116.23811.729
150.5831-0.4758-0.03941.62670.74220.7841-0.0632-0.12350.00510.17570.1256-0.08670.040.0512-0.06240.05620.0165-0.01090.10510.0090.033136.342-2.51716.525
163.2775-0.37261.39811.4703-0.30772.18190.01310.23120.14490.0024-0.0424-0.1915-0.01590.40770.02930.02370.0040.02060.1106-0.00890.081146.765-13.4425.318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 70
2X-RAY DIFFRACTION2A71 - 99
3X-RAY DIFFRACTION3A100 - 213
4X-RAY DIFFRACTION4A214 - 263
5X-RAY DIFFRACTION5B-2 - 70
6X-RAY DIFFRACTION6B71 - 99
7X-RAY DIFFRACTION7B100 - 214
8X-RAY DIFFRACTION8B215 - 263
9X-RAY DIFFRACTION9C0 - 72
10X-RAY DIFFRACTION10C73 - 99
11X-RAY DIFFRACTION11C100 - 214
12X-RAY DIFFRACTION12C215 - 263
13X-RAY DIFFRACTION13D-2 - 70
14X-RAY DIFFRACTION14D71 - 101
15X-RAY DIFFRACTION15D102 - 214
16X-RAY DIFFRACTION16D215 - 263

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