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- PDB-2jjg: Crystal structure of the M. tuberculosis Lysine-epsilon aminotran... -

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Basic information

Entry
Database: PDB / ID: 2jjg
TitleCrystal structure of the M. tuberculosis Lysine-epsilon aminotransferase (Rv3290c) complexed to an inhibitor
ComponentsL-LYSINE EPSILON AMINOTRANSFERASE
KeywordsTRANSFERASE / INHIBITOR COMPLEX / PYRIDOXAL PHOSPHATE / LYSINE AMINO TRANSFERASE
Function / homology
Function and homology information


L-lysine 6-transaminase / L-lysine 6-transaminase activity / : / gamma-aminobutyric acid catabolic process / antibiotic biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
L-lysine 6-transaminase / : / 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 ...L-lysine 6-transaminase / : / 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-L18 / PYRIDOXAL-5'-PHOSPHATE / Probable L-lysine-epsilon aminotransferase / L-lysine-epsilon aminotransferase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsTripathi, S.M. / Ramachandran, R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Mutational Analysis of Mycobacterium Tuberculosis Lysine Epsilon-Aminotransferase and Inhibitor Co-Crystal Structures, Reveals Distinct Binding Modes.
Authors: Tripathi, S.M. / Agarwal, A. / Ramachandran, R.
History
DepositionApr 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 25, 2017Group: Database references / Other / Structure summary
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-LYSINE EPSILON AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5763
Polymers49,0691
Non-polymers5072
Water1,946108
1
A: L-LYSINE EPSILON AMINOTRANSFERASE
hetero molecules

A: L-LYSINE EPSILON AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1516
Polymers98,1382
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area10340 Å2
ΔGint-53.6 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.037, 103.037, 98.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein L-LYSINE EPSILON AMINOTRANSFERASE / LYSINE EPSILON AMINOTRANSFERASE / L-LYSINE AMINOTRANSFERASE / LYSINE 6-AMINOTRANSFERASE


Mass: 49068.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P63509, UniProt: P9WQ77*PLUS, L-lysine 6-transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-L18 / (2S)-1-methyl-2-[(2S,4R)-2-methyl-4-phenylpentyl]piperidine


Mass: 259.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Nonpolymer details3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (L18): INHIBITOR WITH ALTERNATE CONFORMATIONS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.59 % / Description: NONE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20.47 Å / Num. obs: 22549 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.5

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.4→89.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.733 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INHIBITOR COMPLEX WITH PDB 2CIN. THE INHIBTOR HAS ALTERNATE CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1157 5.1 %RANDOM
Rwork0.16 ---
obs0.163 21385 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.17 Å20 Å2
2---0.33 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 34 108 3492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9714725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53922.625160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09415534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7911536
X-RAY DIFFRACTIONr_chiral_restr0.0990.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022676
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21505
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22378
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.290
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5411.52217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94423478
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.50731389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5364.51247
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 112
Rwork0.231 1594

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