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- PDB-1ekp: CRYSTAL STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFE... -

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Entry
Database: PDB / ID: 1ekp
TitleCRYSTAL STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL) COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE AT 2.5 ANGSTROMS (MONOCLINIC 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 / branched-chain amino acid biosynthetic process / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / 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 / branched-chain amino acid biosynthetic process / L-isoleucine catabolic process / branched-chain-amino-acid transaminase / 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
PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsYennawar, N.H. / Dunbar, J.H. / Conway, M. / Hutson, S.M. / Farber, G.K.
Citation
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.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1997
Title: Cloning of the Rat and Human Mitochondrial Branched Chain Aminotransferases (BCATm)
Authors: Bledsoe, R.K. / Dawson, P.A. / Hutson, S.M.
History
DepositionMar 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)83,2304
Polymers82,7362
Non-polymers4942
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-31 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.630, 111.640, 59.900
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL ASSEMBLY IS A DIMER CONSTRUCTED FROM CHAINS A AND B.

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Components

#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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG1500, DTT, HEPES; NA OR K PHOSPHATE, DTT, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.5 mg/mlprotein1drop
250 mmHEPES1drop
320 mMdithiothreitol1drop
450 mMEDTA1drop
51.6 Msodium phosphate1reservoiror potassium phosphate
620 mMdithiothreitol1reservoir
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 22, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40.65 Å / Num. all: 27035 / Num. obs: 21222 / % possible obs: 79.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.632 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.35 % / Rmerge(I) obs: 0.203 / % possible all: 66.8
Reflection
*PLUS
Num. all: 27009 / % possible obs: 78.6 %
Reflection shell
*PLUS
% possible obs: 66.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: E. COLI BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE

Resolution: 2.5→40.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 320233.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1617 7.8 %RANDOM
Rwork0.155 ---
all0.172 27035 --
obs0.166 20603 76.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.37 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.1 Å2
2--0.58 Å20 Å2
3----0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5820 0 30 196 6046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it3.222
X-RAY DIFFRACTIONc_scbond_it3.392
X-RAY DIFFRACTIONc_scangle_it4.672.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 233 8.3 %
Rwork0.198 2589 -
obs--63.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 27009 / Num. reflection obs: 21221 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.332
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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