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- PDB-3tft: Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) f... -

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Basic information

Entry
Database: PDB / ID: 3tft
TitleCrystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, pre-reaction complex with a 3,6-dihydropyrid-2-one heterocycle inhibitor
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
KeywordsTRANSFERASE / PLP
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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsGeders, T.W. / Finzel, B.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Mechanism-based Inactivation by Aromatization of the Transaminase BioA Involved in Biotin Biosynthesis in Mycobaterium tuberculosis.
Authors: Shi, C. / Geders, T.W. / Park, S.W. / Wilson, D.J. / Boshoff, H.I. / Abayomi, O. / Barry, C.E. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)97,6455
Polymers97,0732
Non-polymers5723
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-79 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.057, 66.385, 203.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 48536.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RP / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: bioA, MT1619, MTCY336.35c, Rv1568 / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2
References: UniProt: P0A4X6, UniProt: P9WQ81*PLUS, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 25 mM HEPES pH 7.5, 50 mM NaCl, 0.1 mM TCEP Reservoir:10% PEG 8000, 0.1M magnesium chloride, 0.1M HEPES pH 7.5 Cryo: 15% PEG 400 in reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 27, 2011
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.95→40.33 Å / Num. all: 63139 / Num. obs: 62634 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.16 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.97 / Net I/σ(I): 19.9 / Scaling rejects: 3391
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.95-2.027.220.12511.94489361890.83100
2.02-2.17.230.10613.64532862490.82100
2.1-2.27.240.096154521262170.84100
2.2-2.317.260.08916.34552562430.85100
2.31-2.467.280.0916.44591262840.82100
2.46-2.657.320.09716.44597162590.92100
2.65-2.917.350.0819.54638762910.9100
2.91-3.337.330.06125.64681863480.95100
3.33-4.27.050.0729.54586363711.4499.5
4.2-40.336.330.05537.14011661831.4193.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.51 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.33 Å
Translation2.5 Å40.33 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.0W9Rdata scaling
d*TREK9.9.8.0W9Rdata reduction
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BV0

3bv0


Resolution: 1.95→40.33 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8915 / SU ML: 0.44 / Isotropic thermal model: Isotropic / σ(F): 1.44 / Phase error: 17.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3170 5.06 %Random
Rwork0.1557 ---
all0.1579 63139 --
obs0.1579 62631 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.941 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 84.84 Å2 / Biso mean: 21.0623 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.9303 Å20 Å20 Å2
2--0.4071 Å2-0 Å2
3---0.5232 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6335 0 34 822 7191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076590
X-RAY DIFFRACTIONf_angle_d1.059024
X-RAY DIFFRACTIONf_chiral_restr0.071036
X-RAY DIFFRACTIONf_plane_restr0.0051158
X-RAY DIFFRACTIONf_dihedral_angle_d12.5792295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97910.22481330.160525472680100
1.9791-2.010.19841260.15325952721100
2.01-2.0430.231480.154225532701100
2.043-2.07820.23191310.153925642695100
2.0782-2.1160.23581400.15925652705100
2.116-2.15670.20031400.160525712711100
2.1567-2.20070.20121340.146425622696100
2.2007-2.24860.20591220.141726192741100
2.2486-2.30090.191390.14425792718100
2.3009-2.35840.20911480.150525642712100
2.3584-2.42220.23031260.163825912717100
2.4222-2.49340.22091270.157625862713100
2.4934-2.57390.20791350.15825962731100
2.5739-2.66590.19221400.157826042744100
2.6659-2.77260.20711350.157626052740100
2.7726-2.89870.21511300.165326032733100
2.8987-3.05150.21631270.169626242751100
3.0515-3.24260.20871290.167126172746100
3.2426-3.49280.20071550.159826302785100
3.4928-3.84410.16241420.147826232765100
3.8441-4.39980.14511500.13012594274499
4.3998-5.5410.17471720.14162592276497
5.541-40.3430.22531410.19512477261888

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