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- PDB-3dtg: Structural analysis of mycobacterial branched chain aminotransfer... -

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Basic information

Entry
Database: PDB / ID: 3dtg
TitleStructural analysis of mycobacterial branched chain aminotransferase- implications for inhibitor design
ComponentsBranched-chain amino acid aminotransferase
KeywordsTRANSFERASE / open twisted alpha/beta / Aminotransferase
Function / homology
Function and homology information


branched-chain amino acid metabolic process / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / 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 transaminase activity / L-leucine biosynthetic process / valine biosynthetic process ...branched-chain amino acid metabolic process / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / 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 transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / amino acid 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
O-benzylhydroxylamine / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCastell, A. / Unge, T.
CitationJournal: To be Published
Title: Structural analysis of mycobacterial branched chain aminotransferase - implications for inhibitor design
Authors: Castell, A. / Unge, T.
History
DepositionJul 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_scattering_type / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Branched-chain amino acid aminotransferase
B: Branched-chain amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5347
Polymers80,7322
Non-polymers8025
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-29 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.000, 87.800, 72.900
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Branched-chain amino acid aminotransferase


Mass: 40366.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: ilvE, MSMEG_4276 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: A0R066, branched-chain-amino-acid 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-OBZ / O-benzylhydroxylamine


Mass: 123.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM MES-HCl pH 5.5, 300mM Lithium sulfate, 30% (w/v) PEG 4000 , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 57032 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.11 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / Num. unique all: 30903 / Rsym value: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTF

3dtf


Resolution: 1.9→17 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2851 -random
Rwork0.238 ---
all-56969 --
obs-54118 95 %-
Displacement parametersBiso mean: 19.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 50 256 5866
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it1.2
X-RAY DIFFRACTIONc_mcangle_it1.8

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