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- PDB-6wnn: Bacillus subtilis BioA in complex with amino donor L-Lys -

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Basic information

Entry
Database: PDB / ID: 6wnn
TitleBacillus subtilis BioA in complex with amino donor L-Lys
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
KeywordsTRANSFERASE / DAPA synthase / biotin biosynthesis / lysine aminotransferase / omega aminotransferase
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-LLP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSouza, S.A. / Ng, H.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1833181 United States
CitationJournal: To Be Published
Title: Substrate divergence in 7,8-diaminopelargonic acid synthesis: mutagenesis and computational studies of L-lysine dependent Bacillus subtilis BioA
Authors: Cramer, J. / Kubota, C. / Souza, S.A. / Morris, J. / Ng, H.L. / Sun, R. / Jarrett, J.T.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 15, 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: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6304
Polymers102,0072
Non-polymers6232
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-63 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.300, 60.540, 62.720
Angle α, β, γ (deg.)96.150, 106.040, 99.230
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / 7 / 8-diamino-pelargonic acid aminotransferase / DAPA aminotransferase / 8-diaminononanoate ...7 / 8-diamino-pelargonic acid aminotransferase / DAPA aminotransferase / 8-diaminononanoate synthase / DANS / Diaminopelargonic acid synthase


Mass: 51003.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bioA, A3772_16240, B4417_0368 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A162RZA9, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-LLP / (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid / N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE


Type: L-peptide linking / Mass: 375.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N3O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 30, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.59→59.51 Å / Num. obs: 23055 / % possible obs: 91.7 % / Redundancy: 2.781 % / Biso Wilson estimate: 48.864 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.134 / Χ2: 0.876 / Net I/σ(I): 7.8 / Num. measured all: 64122 / Scaling rejects: 188
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.59-2.651.8840.7541.182457187613040.5520.98969.5
2.65-2.732.7710.6751.714464179416110.7630.82289.8
2.73-2.82.790.5812.144201176115060.8060.70585.5
2.8-2.892.820.442.754487174315910.8930.53191.3
2.89-2.992.8460.3823.24425163115550.9150.4695.3
2.99-3.092.8350.2964.024337161515300.9410.35894.7
3.09-3.212.7870.2265.174122154214790.9540.27295.9
3.21-3.342.8090.1726.463969150114130.9710.20994.1
3.34-3.492.7290.1447.613654144813390.9720.17692.5
3.49-3.662.8350.1198.843671134412950.9840.14596.4
3.66-3.852.8930.09710.663692131712760.9870.11896.9
3.85-4.092.9640.07712.853450120811640.9890.09496.4
4.09-4.372.9290.06713.883199115910920.9910.08294.2
4.37-4.722.8130.06214.54280710629980.9910.07694
4.72-5.172.9190.06314.75281110029630.990.07796.1
5.17-5.782.8380.06813.3724158938510.9890.08495.3
5.78-6.682.8420.06214.4320637847260.9910.07792.6
6.68-8.182.9230.05116.4818216696230.9950.06393.1
8.18-11.562.7760.04118.413275224780.9940.05191.6
11.56-59.512.8740.04719.677502802610.9910.05893.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DOD

3dod


Resolution: 2.59→59.51 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.836 / SU B: 25.246 / SU ML: 0.509 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.495 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3327 1157 5 %RANDOM
Rwork0.2315 ---
obs0.2367 21897 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.54 Å2 / Biso mean: 46.331 Å2 / Biso min: 15.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å2-0.01 Å2
2--0.08 Å2-0.23 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2.59→59.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6577 0 41 0 6618
Biso mean--63.65 --
Num. residues----836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196753
X-RAY DIFFRACTIONr_bond_other_d0.0020.026494
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.989111
X-RAY DIFFRACTIONr_angle_other_deg1.012315024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7085832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54524.881295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.592151227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3171526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021447
LS refinement shellResolution: 2.59→2.653 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.58 58 -
Rwork0.474 1241 -
obs--69.43 %

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