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- PDB-1kta: HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE : THREE DIMENSIO... -

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Basic information

Entry
Database: PDB / ID: 1kta
TitleHUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE : THREE DIMENSIONAL STRUCTURE OF THE ENZYME IN ITS PYRIDOXAMINE PHOSPHATE FORM.
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 / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / L-leucine-2-oxoglutarate transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / Branched-chain amino acid catabolism / 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
ACETIC ACID / 3-METHYL-2-OXOBUTANOIC ACID / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYennawar, N.H. / Conway, M.E. / Yennawar, H.P. / Farber, G.K. / Hutson, S.M.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms
Authors: Yennawar, N.H. / Conway, M.E. / Yennawar, H.P. / Farber, G.K. / Hutson, S.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The Structure of Human Mitochondrial Branched-Chain Aminotransferase
Authors: Yennawar, N. / Dunbar, J. / Conway, M. / Hutson, S. / Farber, G.
#2: Journal: Biochim.Biophys.Acta / Year: 1997
Title: Cloning of the Rat and Human Mitochondrial Branched Amino Acid Aminotransferase (Bcatm).
Authors: Bledsoe, R.K. / Dawson, P.A. / Hutson, S.M.
History
DepositionJan 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)83,86113
Polymers82,7362
Non-polymers1,12511
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-25 kcal/mol
Surface area28310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.450, 105.308, 107.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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)


Mass: 41368.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: O15382, branched-chain-amino-acid transaminase

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Non-polymers , 5 types, 254 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-KIV / 3-METHYL-2-OXOBUTANOIC ACID / ALPHA-KETOISOVALERIC ACID / KETOVALINE


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growpH: 6.9 / Details: pH 6.90
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: Yennawar, N., (2001) Acta Crystallogr., Sect.D, 57, 506.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
250 mMHEPES1drop
320 mMdithiothreitol1drop
450 mMEDTA1drop
522-30 %PEG15001reservoir
6100 mMHEPES1reservoir
720 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 223 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0721
DetectorDetector: CCD / Date: Apr 20, 1999
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 62273 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 0.215
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 0.022 / % possible all: 91.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 246448
Reflection shell
*PLUS
% possible obs: 91.1 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2153684.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: THE ATOMS OF THE HET GROUP KIV REPRESENT THE PRODUCT, KETO ISO VALERATE OF THE REACTION. THESE ATOMS APPEAR ONLY AT LOW CONTOUR LEVELS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3077 5 %RANDOM
Rwork0.24 ---
obs-61024 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6841 Å2 / ksol: 0.333217 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.24 Å20 Å20 Å2
2---3.02 Å20 Å2
3---9.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5820 0 74 243 6137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.672.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 483 5 %
Rwork0.294 9148 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PMP.PARAMPMP.TOP
X-RAY DIFFRACTION4ACY+GLYC.PARAMACY+GLYC.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3

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