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- PDB-3jz6: Crystal structure of Mycobacterium smegmatis Branched Chain Amino... -

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Basic information

Entry
Database: PDB / ID: 3jz6
TitleCrystal structure of Mycobacterium smegmatis Branched Chain Aminotransferase in complex with pyridoxal-5'-phosphate at 1.9 angstrom.
ComponentsBranched-chain amino acid aminotransferase
KeywordsTRANSFERASE / 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
PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCastell, A. / Mille, C. / Unge, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structural analysis of mycobacterial branched-chain aminotransferase: implications for inhibitor design.
Authors: Castell, A. / Mille, C. / Unge, T.
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 5, 2010ID: 3DTH
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 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)81,6736
Polymers80,9952
Non-polymers6784
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-29 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.390, 88.590, 72.890
Angle α, β, γ (deg.)90.000, 105.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Branched-chain amino acid aminotransferase


Mass: 40497.414 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.32 Å3/Da / Density % sol: 46.95 % / Mosaicity: 0.72 °
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200mM MES pH 5.5, 50% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→70.196 Å / Num. all: 51118 / Num. obs: 50840 / % possible obs: 87 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.053 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5021 / Rsym value: 0.14 / % possible all: 76

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTF

3dtf


Resolution: 1.9→25 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2550 4.4 %random
Rwork0.2 ---
all-50840 --
obs-50724 87.1 %-
Solvent computationBsol: 50.706 Å2
Displacement parametersBiso max: 69.21 Å2 / Biso mean: 25.269 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1--8.426 Å20 Å2-7.036 Å2
2--6.136 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 42 454 6056
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.111
X-RAY DIFFRACTIONc_mcbond_it1.2791.5
X-RAY DIFFRACTIONc_scbond_it2.0042
X-RAY DIFFRACTIONc_mcangle_it1.9562
X-RAY DIFFRACTIONc_scangle_it2.9212.5
LS refinement shellResolution: 1.9→2 Å
RfactorNum. reflection% reflection
Rfree0.23 2550 -
Rwork0.2 --
obs-48174 82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_paramprotein_top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ligandm_paramligandm_top

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