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- PDB-5bwu: X-RAY CRYSTAL STRUCTURE AT 2.17A RESOLUTION OF HUMAN MITOCHONDRIA... -

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Basic information

Entry
Database: PDB / ID: 5bwu
TitleX-RAY CRYSTAL STRUCTURE AT 2.17A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TRIAZOLOPYRIMIDINONE 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 / isoleucine catabolic process / branched-chain amino acid biosynthetic process / L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / : / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / isoleucine catabolic process / branched-chain amino acid biosynthetic process / L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / : / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / 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-4VR / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.17 Å
AuthorsSomers, D.O.
CitationJournal: J.Med.Chem. / Year: 2015
Title: The Discovery of in Vivo Active Mitochondrial Branched-Chain Aminotransferase (BCATm) Inhibitors by Hybridizing Fragment and HTS Hits.
Authors: Bertrand, S.M. / Ancellin, N. / Beaufils, B. / Bingham, R.P. / Borthwick, J.A. / Boullay, A.B. / Boursier, E. / Carter, P.S. / Chung, C.W. / Churcher, I. / Dodic, N. / Fouchet, M.H. / ...Authors: Bertrand, S.M. / Ancellin, N. / Beaufils, B. / Bingham, R.P. / Borthwick, J.A. / Boullay, A.B. / Boursier, E. / Carter, P.S. / Chung, C.W. / Churcher, I. / Dodic, N. / Fouchet, M.H. / Fournier, C. / Francis, P.L. / Gummer, L.A. / Herry, K. / Hobbs, A. / Hobbs, C.I. / Homes, P. / Jamieson, C. / Nicodeme, E. / Pickett, S.D. / Reid, I.H. / Simpson, G.L. / Sloan, L.A. / Smith, S.E. / Somers, D.O. / Spitzfaden, C. / Suckling, C.J. / Valko, K. / Washio, Y. / Young, R.J.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)85,53820
Polymers83,4512
Non-polymers2,08818
Water11,764653
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint13 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.343, 106.221, 107.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41725.391 Da / Num. of mol.: 2 / Fragment: residues 28-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, BCT2, ECA40 / Plasmid: pET-28A / Production host: Escherichia coli (E. coli)
References: UniProt: O15382, 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-4VR / 2-[(4-bromobenzyl)amino]-5-propyl[1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one


Mass: 362.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16BrN5O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: MDL Morpheus screen condition B2 + 10mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 12, 2011
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.17→40 Å / Num. obs: 42396 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.941 / Net I/av σ(I): 15.372 / Net I/σ(I): 10.2 / Num. measured all: 158191
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.17-2.213.70.47720780.99599.9
2.21-2.253.70.43921211.027100
2.25-2.293.70.41220910.99399.9
2.29-2.343.80.35221041.018100
2.34-2.393.70.3332105199.6
2.39-2.443.70.31321030.972100
2.44-2.513.70.25921241.03499.9
2.51-2.573.70.22521080.97599.8
2.57-2.653.80.20521110.97399.8
2.65-2.733.80.16221040.99599.6
2.73-2.833.70.1521290.97199.9
2.83-2.943.80.12521021.01199.7
2.94-3.083.70.09821410.98899.7
3.08-3.243.80.07521281.27199.6
3.24-3.443.80.05821180.88798.8
3.44-3.713.70.04821330.91898.9
3.71-4.083.70.03921420.73298.5
4.08-4.673.70.03421420.67398.9
4.67-5.883.70.03321580.61697.9
5.88-403.60.03721540.76392.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.17→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2134 / WRfactor Rwork: 0.1616 / FOM work R set: 0.8467 / SU B: 5.713 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2493 / SU Rfree: 0.1999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1704 4 %RANDOM
Rwork0.17 ---
obs0.1723 40624 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 113.15 Å2 / Biso mean: 36.015 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0 Å2
2--0.23 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 2.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 0 130 653 6478
Biso mean--37.01 42.35 -
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195968
X-RAY DIFFRACTIONr_bond_other_d0.0010.025779
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9828069
X-RAY DIFFRACTIONr_angle_other_deg0.753313272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2695707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86523.385260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4881544
X-RAY DIFFRACTIONr_chiral_restr0.0780.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021360
X-RAY DIFFRACTIONr_mcbond_it2.6884.5052840
X-RAY DIFFRACTIONr_mcbond_other2.6844.5042839
X-RAY DIFFRACTIONr_mcangle_it4.0987.5733540
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 108 -
Rwork0.217 2946 -
all-3054 -
obs--99.77 %

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