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- PDB-4wyd: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase from M... -

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Basic information

Entry
Database: PDB / ID: 4wyd
TitleAdenosylmethionine-8-amino-7-oxononanoate aminotransferase from Mycobacterium tuberculosis complexed with a fragment from DSF screening
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
Keywordstransferase/transferase inhibitor / transaminase PLP Complex 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-3VR / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDai, R. / Finzel, B.C. / 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 15, 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_oper_list / refine_hist
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_oper_list.symmetry_operation / _refine_hist.d_res_high / _refine_hist.d_res_low

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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)99,12919
Polymers97,0732
Non-polymers2,05617
Water17,024945
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-38 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.104, 66.49, 204.65
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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 (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

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Non-polymers , 5 types, 962 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-3VR / N-methyl-1-[4-(1H-pyrazol-1-ylmethyl)phenyl]methanamine


Mass: 201.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N3
#4: 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
#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.: 945 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
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: 1.35→32.815 Å / Num. obs: 189156 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.66 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.7
Reflection shellHighest resolution: 1.35 Å

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Processing

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

3tft


Resolution: 1.35→32.815 Å / SU ML: 0.106228501064 / Cross valid method: FREE R-VALUE / σ(F): 1.349 / Phase error: 13.2139769654
RfactorNum. reflection% reflection
Rfree0.1576 9502 5.02336695637 %
Rwork0.126 179654 -
obs0.127 189156 99.9402966149 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.271368792 Å2
Refinement stepCycle: LAST / Resolution: 1.35→32.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 134 945 7510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005791729279537059
X-RAY DIFFRACTIONf_angle_d1.092063284829697
X-RAY DIFFRACTIONf_chiral_restr0.07211255780091111
X-RAY DIFFRACTIONf_plane_restr0.005411650146491246
X-RAY DIFFRACTIONf_dihedral_angle_d13.02047254232531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.1914757187773170.1548157765495905X-RAY DIFFRACTION99.9678663239
1.3653-1.38140.2063792629262950.1512808750235936X-RAY DIFFRACTION99.8557692308
1.3814-1.39830.1950785779543410.147963245115875X-RAY DIFFRACTION99.9678353168
1.3983-1.4160.1898911891063350.142038264495955X-RAY DIFFRACTION99.9682136046
1.416-1.43460.1649744201273070.1348508220245939X-RAY DIFFRACTION99.936
1.4346-1.45420.1810192363733030.1315754797175938X-RAY DIFFRACTION99.9839794938
1.4542-1.4750.1595987906813040.1247875692835968X-RAY DIFFRACTION99.9681224099
1.475-1.4970.1652903766273340.1188799582675848X-RAY DIFFRACTION99.9838266214
1.497-1.52040.1542192042883130.1156399898285956X-RAY DIFFRACTION99.9681071599
1.5204-1.54530.1482691108963000.1131444983595983X-RAY DIFFRACTION99.9840865691
1.5453-1.5720.1471202318683070.1147390220355918X-RAY DIFFRACTION100
1.572-1.60060.153181340133010.1080766416795972X-RAY DIFFRACTION100
1.6006-1.63140.142657754773200.1063961865695929X-RAY DIFFRACTION99.9520153551
1.6314-1.66470.1432064366542810.1105636208886030X-RAY DIFFRACTION99.9524865379
1.6647-1.70090.1622616747272840.1147742438375993X-RAY DIFFRACTION99.9681477942
1.7009-1.74040.1574351900343060.1217252601775941X-RAY DIFFRACTION99.952
1.7404-1.78390.1531230315663060.1197429205535949X-RAY DIFFRACTION99.9360920275
1.7839-1.83220.1496912731293450.1166223212715967X-RAY DIFFRACTION99.9683243586
1.8322-1.88610.1484916090252860.1146333119365991X-RAY DIFFRACTION99.9363158733
1.8861-1.94690.1562611327273310.1198707328625970X-RAY DIFFRACTION100
1.9469-2.01650.1604205611823190.1271447400095991X-RAY DIFFRACTION99.9050031666
2.0165-2.09720.1605957399073170.1258397667075994X-RAY DIFFRACTION99.9524865379
2.0972-2.19270.1649286889423150.1253940075325985X-RAY DIFFRACTION99.9682640432
2.1927-2.30830.1429833861863290.1216053753616008X-RAY DIFFRACTION99.9369184671
2.3083-2.45280.1524084587833400.1297285376795998X-RAY DIFFRACTION99.9054224464
2.4528-2.64210.1645131718083430.1341438725386043X-RAY DIFFRACTION99.9530442949
2.6421-2.90790.1535340060223270.1359308248836040X-RAY DIFFRACTION99.8901788516
2.9079-3.32830.1571810445593030.1321409940926128X-RAY DIFFRACTION99.8757571051
3.3283-4.19190.1738465641663650.1227962361136110X-RAY DIFFRACTION99.8457979954
4.1919-32.82450.1384831845063280.1285553360566394X-RAY DIFFRACTION99.747737053

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