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- PDB-1ekf: CRYSTALLOGRAPHIC STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMI... -

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Basic information

Entry
Database: PDB / ID: 1ekf
TitleCRYSTALLOGRAPHIC STRUCTURE OF HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL) COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE AT 1.95 ANGSTROMS (ORTHORHOMBIC 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 / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / Branched-chain amino acid catabolism ...regulation of hormone levels / branched-chain-amino-acid transaminase activity / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / Branched-chain amino acid catabolism / L-leucine biosynthetic process / 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 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal ...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 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / 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 / SYNCHROTRON / Resolution: 1.95 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 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 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
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-31 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.385, 105.032, 107.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A and chain 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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.519 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG1500, HEPES, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
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: 1.0721203
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: 1.0721203 Å / Relative weight: 1
ReflectionResolution: 1.95→24.29 Å / Num. all: 57217 / Num. obs: 48329 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.81 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.34
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.414 / % possible all: 63.8
Reflection shell
*PLUS
% possible obs: 63.8 %

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Processing

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

Resolution: 1.95→24.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 199264.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: THE DENSITY FOR LOOP 172 TO 179 IN MONOMER A IS WEAK. THE DENSITY FOR THE SAME LOOP IN MONOMER B IS GOOD.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3985 8.2 %RANDOM
Rwork0.222 ---
all0.242 57217 --
obs0.232 48329 83.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.13 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.11 Å20 Å20 Å2
2---0.38 Å20 Å2
3---8.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5820 0 30 273 6123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.07
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 525 8.7 %
Rwork0.264 5517 -
obs--63.8 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.584
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07

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