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- PDB-5i60: X-RAY CRYSTAL STRUCTURE AT 2.12A RESOLUTION OF HUMAN MITOCHONDRIA... -

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Basic information

Entry
Database: PDB / ID: 5i60
TitleX-RAY CRYSTAL STRUCTURE AT 2.12A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIARL AMIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.
ComponentsBranched-chain-amino-acid aminotransferase, mitochondrial
KeywordsTRANSFERASE / FOLD TYPE IV
Function / homology
Function and homology information


regulation of hormone levels / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / Branched-chain amino acid catabolism / L-valine biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm
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 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes ...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 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / 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-67W / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.12 Å
AuthorsSomers, D.O.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening.
Authors: Borthwick, J.A. / Ancellin, N. / Bertrand, S.M. / Bingham, R.P. / Carter, P.S. / Chung, C.W. / Churcher, I. / Dodic, N. / Fournier, C. / Francis, P.L. / Hobbs, A. / Jamieson, C. / Pickett, S. ...Authors: Borthwick, J.A. / Ancellin, N. / Bertrand, S.M. / Bingham, R.P. / Carter, P.S. / Chung, C.W. / Churcher, I. / Dodic, N. / Fournier, C. / Francis, P.L. / Hobbs, A. / Jamieson, C. / Pickett, S.D. / Smith, S.E. / Somers, D.O. / Spitzfaden, C. / Suckling, C.J. / Young, R.J.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2May 1, 2024Group: 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, mitochondrial
B: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,21717
Polymers83,4512
Non-polymers1,76615
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-23 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.296, 106.629, 106.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCAT(m) / Placental protein 18 / PP18


Mass: 41725.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, BCT2, ECA40 / Production host: Escherichia coli (E. coli)
References: UniProt: O15382, branched-chain-amino-acid transaminase

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Non-polymers , 5 types, 506 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-67W / (2-{[4-(1H-pyrazol-3-yl)phenyl]carbamoyl}phenyl)acetic acid


Mass: 321.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15N3O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MDL MORPHEUS SCREEN CONDITION B2, DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.12→40 Å / Num. obs: 45566 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.077 / Net I/av σ(I): 24.202 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.12-2.167.10.5791100
2.16-2.27.20.5421100
2.2-2.247.20.4611100
2.24-2.287.20.4041100
2.28-2.337.10.3431100
2.33-2.397.20.3081100
2.39-2.457.10.2991100
2.45-2.517.10.2521100
2.51-2.597.10.221100
2.59-2.677.10.1991100
2.67-2.777.20.1681100
2.77-2.887.10.1511100
2.88-3.017.10.1271100
3.01-3.1770.1011100
3.17-3.3670.0761100
3.36-3.626.70.0571100
3.62-3.996.80.0481100
3.99-4.577.20.0411100
4.57-5.757.10.0391100
5.75-406.70.036199.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: In-house structure

Resolution: 2.12→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.257 / SU ML: 0.136 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.187
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1827 4 %RANDOM
Rwork0.164 ---
obs0.1665 43388 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.91 Å2 / Biso mean: 41.319 Å2 / Biso min: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å2-0 Å2-0 Å2
2--0.75 Å2-0 Å2
3---1.2 Å2
Refinement stepCycle: final / Resolution: 2.12→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5727 0 116 491 6334
Biso mean--50.09 46.36 -
Num. residues----716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195991
X-RAY DIFFRACTIONr_bond_other_d0.0020.025800
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9828111
X-RAY DIFFRACTIONr_angle_other_deg0.759313320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2545714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39723.308260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.123151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.811544
X-RAY DIFFRACTIONr_chiral_restr0.0790.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216639
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021399
X-RAY DIFFRACTIONr_mcbond_it3.295.1132864
X-RAY DIFFRACTIONr_mcbond_other3.2845.1112861
X-RAY DIFFRACTIONr_mcangle_it4.8448.5913571
LS refinement shellResolution: 2.12→2.174 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 132 -
Rwork0.226 3126 -
all-3258 -
obs--100 %

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