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

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Basic information

Entry
Database: PDB / ID: 4xew
TitleCrystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a HTS lead compound
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
Chem-40N / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 Å
AuthorsFinzel, B.C. / Dai, R.
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
DepositionDec 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 2.0Jan 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _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 / _struct_site_gen.auth_seq_id
Revision 2.1Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)98,1346
Polymers97,0732
Non-polymers1,0614
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-84 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.755, 66.153, 203.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 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 (strain ATCC 25618 / H37Rv) (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
#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-40N / 6-(2-fluorophenyl)[1,3]dioxolo[4,5-g]quinolin-8(5H)-one


Mass: 283.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10FNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
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: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.47→101.63 Å / Num. obs: 28186 / % possible obs: 94.08 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.3
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 6.2 / % possible all: 79.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREKdata reduction
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TFT

3tft


Resolution: 2.47→101.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.818 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.138 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1507 5.1 %RANDOM
Rwork0.1652 28186 --
obs0.168 28186 94.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.13 Å2 / Biso mean: 22.212 Å2 / Biso min: 6.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---1.24 Å20 Å2
3---1.64 Å2
Refinement stepCycle: final / Resolution: 2.47→101.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 72 212 6688
Biso mean--20.96 20.66 -
Num. residues----856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026792
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.969326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5622.197264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54815994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6881554
X-RAY DIFFRACTIONr_chiral_restr0.090.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215222
LS refinement shellResolution: 2.462→2.525 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 87 -
Rwork0.204 1648 -
all-1735 -
obs--78.51 %

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