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

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Basic information

Entry
Database: PDB / ID: 4wyg
TitleCrystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis complexed with a fragment hit
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
Keywordstransferase/transferase inhibitor / Complex / transaminase / PLP / fragment / 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-3W1 / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDai, R. / Finzel, B.C.
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 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entry_details / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
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 / _struct_keywords.text

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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)99,39220
Polymers97,0732
Non-polymers2,31918
Water15,835879
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-38 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.124, 66.433, 205.318
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 , 5 types, 897 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-3W1 / 1-{4-[(4-chloro-1H-pyrazol-1-yl)methyl]phenyl}methanamine


Mass: 221.686 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12ClN3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.76 %
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: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→46.401 Å / Num. obs: 106327 / % possible obs: 96.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.3

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→46.401 Å / FOM work R set: 0.901 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 5318 5.01 %
Rwork0.1511 100913 -
obs0.1526 106231 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.2 Å2 / Biso mean: 18.64 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.62→46.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 209 879 7508
Biso mean--26.11 30.18 -
Num. residues----858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087291
X-RAY DIFFRACTIONf_angle_d1.14710024
X-RAY DIFFRACTIONf_chiral_restr0.0431124
X-RAY DIFFRACTIONf_plane_restr0.0051294
X-RAY DIFFRACTIONf_dihedral_angle_d13.572612
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 (%)
1.62-1.63840.22211560.17313238339495
1.6384-1.65770.19171720.16773269344194
1.6577-1.67790.18081900.16013231342195
1.6779-1.69910.23281700.16163309347994
1.6991-1.72150.20451800.16343236341695
1.7215-1.74510.21611670.16153295346294
1.7451-1.770.21171780.16223318349696
1.77-1.79640.21891760.16263295347194
1.7964-1.82450.20721820.16413269345196
1.8245-1.85440.20441840.17193301348595
1.8544-1.88640.20951610.16763339350097
1.8864-1.92070.21631740.16753291346595
1.9207-1.95760.19171780.1593370354897
1.9576-1.99760.18922000.16283253345395
1.9976-2.0410.19531710.15843380355196
2.041-2.08850.18071470.15333377352497
2.0885-2.14080.16631460.15273371351796
2.1408-2.19860.19981670.15363361352896
2.1986-2.26330.19061760.15253370354697
2.2633-2.33640.18371730.15093380355396
2.3364-2.41990.18551950.15293367356297
2.4199-2.51680.16681790.15393375355497
2.5168-2.63130.19361710.15723442361397
2.6313-2.770.20571760.15783436361298
2.77-2.94350.18521620.15693444360698
2.9435-3.17080.18312010.15353421362297
3.1708-3.48970.19081930.15013458365198
3.4897-3.99450.14781890.13533484367398
3.9945-5.03170.1272010.11773531373298
5.0317-46.41990.16872030.15053702390598

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