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- PDB-5i5x: X-RAY CRYSTAL STRUCTURE AT 1.65A RESOLUTION OF HUMAN MITOCHONDRIA... -

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Entry
Database: PDB / ID: 5i5x
TitleX-RAY CRYSTAL STRUCTURE AT 1.65A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A THIAZOLE COMPOUND AND PMP 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-68C / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 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)85,89028
Polymers83,4512
Non-polymers2,43926
Water19,1321062
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-69 kcal/mol
Surface area27910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.369, 105.300, 107.156
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 , 6 types, 1088 molecules

#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-68C / 5-methyl-4-oxo-N-(1,3,4-thiadiazol-2-yl)-3,4-dihydrothieno[2,3-d]pyrimidine-6-carboxamide


Mass: 293.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7N5O2S2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1062 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→58.232 Å / Num. obs: 94698 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.081 / Net I/av σ(I): 5.482 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.65-1.7450.5221.4199.5
1.74-1.8450.3432.2199.8
1.84-1.9750.2043.6199.9
1.97-2.1350.1325.5199.9
2.13-2.3350.0987.1199.9
2.33-2.6150.097.21100
2.61-3.0150.0797.51100
3.01-3.694.80.0589.4199.7
3.69-5.224.90.05310.4199
5.22-58.2324.90.0539.9199.6

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
MOSFLM7.0.6data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: In-house structure

Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.24 / SU ML: 0.076 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.105
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 4744 5 %RANDOM
Rwork0.1793 ---
obs0.1815 89874 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.12 Å2 / Biso mean: 22.693 Å2 / Biso min: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.27 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 150 1062 6979
Biso mean--30.75 36.04 -
Num. residues----722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196246
X-RAY DIFFRACTIONr_bond_other_d0.0020.026047
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9858475
X-RAY DIFFRACTIONr_angle_other_deg0.724313907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3755758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27623.309269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.068151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8831546
X-RAY DIFFRACTIONr_chiral_restr0.0770.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217048
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021440
X-RAY DIFFRACTIONr_mcbond_it1.4842.6882987
X-RAY DIFFRACTIONr_mcbond_other1.4832.6882986
X-RAY DIFFRACTIONr_mcangle_it2.3664.5153760
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 335 -
Rwork0.261 6506 -
all-6841 -
obs--99.25 %

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