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- PDB-5u3f: Structure of Mycobacterium tuberculosis IlvE, a branched-chain am... -

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Basic information

Entry
Database: PDB / ID: 5u3f
TitleStructure of Mycobacterium tuberculosis IlvE, a branched-chain amino acid transaminase, in complex with D-cycloserine derivative
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / branched-chain amino acid transaminase / amino acid biosynthesis / Pyridoxal phosphate / inhibitor / D-cycloserine
Function / homology
Function and homology information


L-methionine salvage / branched-chain amino acid metabolic process / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / branched-chain-amino-acid transaminase activity / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process ...L-methionine salvage / branched-chain amino acid metabolic process / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / branched-chain-amino-acid transaminase activity / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal ...Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7TS / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsFavrot, L. / Amorim Franco, T.M. / Blanchard, J.S.
Funding support United States, Brazil, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI060899 United States
Science Without Boarders fellowship CAPES Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior Brazil
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Mechanism-Based Inhibition of the Mycobacterium tuberculosis Branched-Chain Aminotransferase by d- and l-Cycloserine.
Authors: Amorim Franco, T.M. / Favrot, L. / Vergnolle, O. / Blanchard, J.S.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Branched-chain-amino-acid aminotransferase
B: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0764
Polymers79,4142
Non-polymers6622
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-34 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.892, 80.464, 81.250
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 Branched-chain-amino-acid aminotransferase / BCAT


Mass: 39706.910 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: ilvE, Rv2210c, MTCY190.21c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WQ75, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-7TS / (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate


Mass: 331.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 1.89 Å3/Da / Density % sol: 34.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris, pH 6.5 and 25 % w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Jun 11, 2015
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.695→50 Å / Num. obs: 117641 / % possible obs: 91.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.51
Reflection shellResolution: 1.695→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HT5

3ht5


Resolution: 1.695→36.265 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.2099 5880 5 %
Rwork0.1762 --
obs0.1779 117618 91.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.695→36.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 44 618 5640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015162
X-RAY DIFFRACTIONf_angle_d1.2067029
X-RAY DIFFRACTIONf_dihedral_angle_d12.3031839
X-RAY DIFFRACTIONf_chiral_restr0.053766
X-RAY DIFFRACTIONf_plane_restr0.006919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6953-1.71450.29651960.27263765X-RAY DIFFRACTION91
1.7145-1.73470.25512140.2314095X-RAY DIFFRACTION100
1.7347-1.75590.24112150.21174049X-RAY DIFFRACTION100
1.7559-1.77810.25982080.19944066X-RAY DIFFRACTION100
1.7781-1.80150.22682140.19454122X-RAY DIFFRACTION100
1.8015-1.82620.30672180.20574070X-RAY DIFFRACTION100
1.8262-1.85230.30812180.22654108X-RAY DIFFRACTION100
1.8523-1.87990.32562110.29153996X-RAY DIFFRACTION98
1.8799-1.90930.25481580.2352991X-RAY DIFFRACTION94
1.9093-1.94060.921370.5221690X-RAY DIFFRACTION79
1.9406-1.9740.47711440.39492753X-RAY DIFFRACTION67
1.974-2.00990.25332100.19654085X-RAY DIFFRACTION100
2.0099-2.04860.23892140.18254061X-RAY DIFFRACTION100
2.0486-2.09040.24132130.18614071X-RAY DIFFRACTION100
2.0904-2.13580.21482160.1824080X-RAY DIFFRACTION100
2.1358-2.18550.21692200.1734102X-RAY DIFFRACTION100
2.1855-2.24020.20521570.2033036X-RAY DIFFRACTION96
2.2402-2.30070.31971000.24821869X-RAY DIFFRACTION83
2.3007-2.36840.22272130.17624068X-RAY DIFFRACTION99
2.3684-2.44480.19042140.16734085X-RAY DIFFRACTION100
2.4448-2.53220.21462130.17194076X-RAY DIFFRACTION100
2.5322-2.63360.20012150.17544082X-RAY DIFFRACTION100
2.6336-2.75340.20512180.17374036X-RAY DIFFRACTION100
2.7534-2.89850.21162210.17444113X-RAY DIFFRACTION100
2.8985-3.080.20322190.17544084X-RAY DIFFRACTION100
3.08-3.31770.20362140.17254071X-RAY DIFFRACTION100
3.3177-3.65120.19772000.15663865X-RAY DIFFRACTION99
3.6512-4.17890.15671720.15143306X-RAY DIFFRACTION92
4.1789-5.26240.15152120.12274066X-RAY DIFFRACTION100
5.2624-36.27330.15012060.14243877X-RAY DIFFRACTION95

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