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- PDB-5bww: X-RAY CRYSTAL STRUCTURE AT 1.82A RESOLUTION OF HUMAN MITOCHONDRIA... -

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Entry
Database: PDB / ID: 5bww
TitleX-RAY CRYSTAL STRUCTURE AT 1.82A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRROLIDINE 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 / 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-4W6 / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.82 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)85,77425
Polymers83,4512
Non-polymers2,32323
Water12,466692
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-9 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.290, 106.590, 106.810
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 , 7 types, 715 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-4W6 / 7-oxo-2-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile


Mass: 313.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N5O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 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: 1.82→39.316 Å / Num. all: 71091 / Num. obs: 71091 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 27.4 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Rsym value: 0.057 / Net I/av σ(I): 7.709 / Net I/σ(I): 15.1 / Num. measured all: 494827
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.82-1.926.70.4551.268806102760.1860.4553.599.8
1.92-2.036.90.3441.96716097830.1390.3445.3100
2.03-2.187.10.1724.56551992120.0690.1729100
2.18-2.356.30.15735245882680.0650.15711.896.7
2.35-2.577.20.075105752879620.030.07515.8100
2.57-2.887.30.05213.55250972120.0210.05220.3100
2.88-3.327.30.04115.54658963780.0160.04125.5100
3.32-4.077.10.05110.73857354300.020.05130.199.8
4.07-5.767.20.02823.23045142480.0110.02832.299.5
5.76-39.3166.60.0321.61523423220.0130.0329.194.2

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.82→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2695 / WRfactor Rwork: 0.2237 / FOM work R set: 0.7703 / SU B: 3.997 / SU ML: 0.117 / SU R Cruickshank DPI: 0.172 / SU Rfree: 0.1568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 3449 5.1 %RANDOM
Rwork0.2203 ---
obs0.2224 64546 95.01 %-
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: 101.53 Å2 / Biso mean: 34.473 Å2 / Biso min: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2--0.76 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5651 0 150 692 6493
Biso mean--39.44 44.4 -
Num. residues----706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196018
X-RAY DIFFRACTIONr_bond_other_d0.0010.025841
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9898149
X-RAY DIFFRACTIONr_angle_other_deg0.745313414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2865720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54723.282259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.369151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4661546
X-RAY DIFFRACTIONr_chiral_restr0.0790.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021371
X-RAY DIFFRACTIONr_mcbond_it2.5134.212868
X-RAY DIFFRACTIONr_mcbond_other2.5114.2092867
X-RAY DIFFRACTIONr_mcangle_it3.6457.0693592
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 276 -
Rwork0.298 4908 -
all-5184 -
obs--99.83 %

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