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- PDB-5i5u: X-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIA... -

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Basic information

Entry
Database: PDB / ID: 5i5u
TitleX-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TETRAHYDRONAPHTHALENYL 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-67Y / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.404 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)84,95316
Polymers83,4512
Non-polymers1,50214
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-32 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.074, 105.995, 107.462
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, 532 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-67Y / 2-hydroxy-N-[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]acetamide


Mass: 205.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO2
#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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 518 / 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: 47.82 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 4, 2010 / Details: VARIMAX HF
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.404→107.462 Å / Num. obs: 31398 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.088 / Net I/av σ(I): 8.507 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.404-2.535.20.5021.61100
2.53-2.695.20.3642.1199.9
2.69-2.875.30.2433.21100
2.87-3.15.30.1634.71100
3.1-3.45.30.0997.81100
3.4-3.85.20.06312199.8
3.8-4.395.10.04416.8199.8
4.39-5.385.10.03620.21100
5.38-7.64.90.04117.81100
7.6-107.4624.40.02521.8197.7

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Processing

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

Resolution: 2.404→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.302 / SU ML: 0.191 / SU R Cruickshank DPI: 0.5094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.509 / ESU R Free: 0.265
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1579 5 %RANDOM
Rwork0.1671 ---
obs0.1705 29753 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.17 Å2 / Biso mean: 35.289 Å2 / Biso min: 10.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2--0.94 Å2-0 Å2
3---1.07 Å2
Refinement stepCycle: final / Resolution: 2.404→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 96 518 6389
Biso mean--38.93 36.08 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196036
X-RAY DIFFRACTIONr_bond_other_d0.0010.025825
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9828180
X-RAY DIFFRACTIONr_angle_other_deg0.748313390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3085724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66723.308263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.816151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3381545
X-RAY DIFFRACTIONr_chiral_restr0.0770.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021385
X-RAY DIFFRACTIONr_mcbond_it2.94.4842899
X-RAY DIFFRACTIONr_mcbond_other2.8954.4832898
X-RAY DIFFRACTIONr_mcangle_it4.5477.5513622
LS refinement shellResolution: 2.404→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 98 -
Rwork0.233 2155 -
all-2253 -
obs--99.91 %

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