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- PDB-6prx: oxidized Human Branched Chain Aminotransferase mutant C318A -

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Basic information

Entry
Database: PDB / ID: 6prx
Titleoxidized Human Branched Chain Aminotransferase mutant C318A
ComponentsBranched-chain-amino-acid aminotransferase, mitochondrial
KeywordsTRANSFERASE / oxidized / metabolic role / conformational change
Function / homology
Function and homology information


regulation of hormone levels / 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 transaminase activity / Branched-chain amino acid catabolism ...regulation of hormone levels / 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 transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process / amino acid 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 / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsDong, M. / Herbert, D. / Gibbs, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of an oxidized mutant of human mitochondrial branched-chain aminotransferase.
Authors: Herbert, D. / Gibbs, S. / Riddick, A. / Conway, M. / Dong, M.
History
DepositionJul 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)87,2004
Polymers86,7062
Non-polymers4942
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-31 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.204, 104.938, 106.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 3 - 365 / Label seq-ID: 21 - 383

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Branched-chain-amino-acid aminotransferase, mitochondrial / BCAT(m) / Placental protein 18 / PP18


Mass: 43353.070 Da / Num. of mol.: 2 / Mutation: C318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT2, BCATM, BCT2, ECA40 / Production host: Escherichia phage EcSzw-2 (virus)
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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 200 mM magnesium acetate tetrahydrate, 100 mM sodium cacodylate trihydrate pH6.5, 20% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.22→50 Å / Num. obs: 12545 / % possible obs: 99.1 % / Redundancy: 8.8 % / Biso Wilson estimate: 44.14 Å2 / CC1/2: 0.871 / Rpim(I) all: 0.04 / Net I/σ(I): 11.85
Reflection shellResolution: 3.22→3.28 Å / Num. unique obs: 586 / CC1/2: 0.871 / Rpim(I) all: 0.214 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hgw

2hgw


Resolution: 3.25→47.46 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.846 / SU B: 27.973 / SU ML: 0.454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.595
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 602 4.8 %RANDOM
Rwork0.2199 ---
obs0.2218 11943 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.05 Å2 / Biso mean: 40.716 Å2 / Biso min: 27.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 3.25→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5667 0 30 0 5697
Biso mean--46.74 --
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135852
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175514
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.6427944
X-RAY DIFFRACTIONr_angle_other_deg0.9991.56812759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.28121.311305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89615991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3721545
X-RAY DIFFRACTIONr_chiral_restr0.0330.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021255
Refine LS restraints NCS

Ens-ID: 1 / Number: 10731 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.25→3.332 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.326 32 -
Rwork0.298 780 -
obs--87.5 %

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