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- PDB-4wyc: Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) f... -

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Basic information

Entry
Database: PDB / ID: 4wyc
TitleCrystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a thiazole benzamide inhibitor
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
Keywordstransferase/transferase inhibitor / Inhibitor Complex Transaminase PLP / transferase-transferase inhibitor complex
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
4-(1H-imidazol-1-yl)benzamide / FORMYL GROUP / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFinzel, B.C. / Dai, R. / Geders, T.W.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA.
Authors: Dai, R. / Geders, T.W. / Liu, F. / Park, S.W. / Schnappinger, D. / Aldrich, C.C. / Finzel, B.C.
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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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)98,21611
Polymers97,0732
Non-polymers1,1439
Water13,980776
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-107 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.288, 65.982, 203.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: 48536.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: bioA, Rv1568, MTCY336.35c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WQ81, adenosylmethionine-8-amino-7-oxononanoate transaminase

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Non-polymers , 7 types, 785 molecules

#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-3VS / 4-(1H-imidazol-1-yl)benzamide


Mass: 187.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9N3O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 mM HEPES pH 7.5, 50 mM NaCl, 0.1 mM TCEP Reservoir:9% PEG 8000, 0.1M magnesium chloride, 0.1M HEPES pH 7.5 Cryo: 15% PEG 400 in reservoir solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→39.711 Å / Num. obs: 94878 / % possible obs: 98.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.8

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TFT

3tft


Resolution: 1.7→39.711 Å / FOM work R set: 0.8571 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 4750 5.01 %
Rwork0.1737 90010 -
obs0.1757 94760 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.02 Å2 / Biso mean: 17.96 Å2 / Biso min: 3.52 Å2
Refinement stepCycle: final / Resolution: 1.7→39.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 74 779 7261
Biso mean--22.19 27.17 -
Num. residues----857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076974
X-RAY DIFFRACTIONf_angle_d1.1719606
X-RAY DIFFRACTIONf_chiral_restr0.0441099
X-RAY DIFFRACTIONf_plane_restr0.0061241
X-RAY DIFFRACTIONf_dihedral_angle_d13.1072499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.33111320.2922935306799
1.7193-1.73960.32231310.263429673098100
1.7396-1.76080.27331280.257330283156100
1.7608-1.78310.31521440.241629453089100
1.7831-1.80650.28851710.244729673138100
1.8065-1.83130.2981520.242729853137100
1.8313-1.85740.2731670.235329363103100
1.8574-1.88520.2971660.238929443110100
1.8852-1.91460.28421590.22929703129100
1.9146-1.9460.27431590.234829813140100
1.946-1.97960.2551700.221529593129100
1.9796-2.01550.28491580.216529443102100
2.0155-2.05430.25231590.214429823141100
2.0543-2.09620.20761760.187529653141100
2.0962-2.14180.22461460.17329943140100
2.1418-2.19160.18431490.167730103159100
2.1916-2.24640.21341630.162429513114100
2.2464-2.30720.22241860.162329643150100
2.3072-2.37510.21341670.165529893156100
2.3751-2.45170.23881560.170730143170100
2.4517-2.53930.21941580.171530343192100
2.5393-2.6410.20541510.165729973148100
2.641-2.76110.20091570.16630243181100
2.7611-2.90670.22021750.165429643139100
2.9067-3.08870.21981720.159629993171100
3.0887-3.32710.17621640.158930623226100
3.3271-3.66170.18451750.147430513226100
3.6617-4.19110.14961310.133230903221100
4.1911-5.27830.14641650.123631003265100
5.2783-39.72160.18981630.15632593422100

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