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- PDB-5bwt: X-RAY CRYSTAL STRUCTURE AT 2.20A RESOLUTION OF HUMAN MITOCHONDRIA... -

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Basic information

Entry
Database: PDB / ID: 5bwt
TitleX-RAY CRYSTAL STRUCTURE AT 2.20A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRAZOLOPYRIMIDINONE FRAGMENT AND AN INTERNAL ALDIMINE LINKED PLP.
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 / 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 biosynthetic process / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / isoleucine catabolic process / 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 biosynthetic process / Branched-chain amino acid catabolism / L-leucine biosynthetic process / 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 / 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
Chem-4VS / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 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)84,92016
Polymers83,4512
Non-polymers1,47014
Water10,395577
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-40 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.307, 106.628, 108.049
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 / 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

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Non-polymers , 6 types, 591 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-4VS / 5-ethyl-2-methyl-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile


Mass: 202.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N4O
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: Nov 6, 2010
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 41145 / % possible obs: 99.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.133 / Net I/av σ(I): 18.074 / Net I/σ(I): 10.6 / Num. measured all: 220433
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.245.30.45920481.121100
2.24-2.285.30.40620141.104100
2.28-2.325.30.46720351.122100
2.32-2.375.30.40120381.155100
2.37-2.425.40.37720301.103100
2.42-2.485.40.32120501.12100
2.48-2.545.40.27420451.152100
2.54-2.615.40.24320511.122100
2.61-2.695.40.20820361.183100
2.69-2.775.40.17320641.161100
2.77-2.875.40.15620281.204100
2.87-2.995.40.12920671.177100
2.99-3.125.40.10320521.198100
3.12-3.295.40.08720721.209100
3.29-3.495.40.07220701.175100
3.49-3.765.40.06720581.369100
3.76-4.145.40.05421021.09499.9
4.14-4.745.40.04720911.05899.2
4.74-5.975.40.04520890.90998
5.97-405.20.04221050.9393.3

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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: 2.2→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2325 / WRfactor Rwork: 0.1663 / FOM work R set: 0.8157 / SU B: 6.755 / SU ML: 0.167 / SU R Cruickshank DPI: 0.2706 / SU Rfree: 0.2246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 1654 4 %RANDOM
Rwork0.1755 ---
obs0.1785 39394 99.2 %-
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: 108.37 Å2 / Biso mean: 35.549 Å2 / Biso min: 14.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å2-0 Å20 Å2
2--1.51 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5741 0 93 577 6411
Biso mean--37.42 40.44 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196023
X-RAY DIFFRACTIONr_bond_other_d0.0010.025835
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9768166
X-RAY DIFFRACTIONr_angle_other_deg0.771313408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4515722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8523.434265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3281544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021389
X-RAY DIFFRACTIONr_mcbond_it2.7424.4452885
X-RAY DIFFRACTIONr_mcbond_other2.7394.4442884
X-RAY DIFFRACTIONr_mcangle_it4.1157.4733602
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 117 -
Rwork0.251 2816 -
all-2933 -
obs--97.8 %

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