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- PDB-5mpr: Single Amino Acid Variant of Human Mitochondrial Branched Chain A... -

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Basic information

Entry
Database: PDB / ID: 5mpr
TitleSingle Amino Acid Variant of Human Mitochondrial Branched Chain Amino Acid Aminotransferase 2
ComponentsBranched-chain-amino-acid aminotransferase, mitochondrial
KeywordsTRANSFERASE / aminotransferase transaminase PLP mutation
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 / SYNCHROTRON / Resolution: 1.6 Å
AuthorsHakansson, M. / Walse, B. / Nilsson, C. / Anderson, L.C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Sweden
CitationJournal: J. Am. Soc. Mass Spectrom. / Year: 2017
Title: Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2).
Authors: Anderson, L.C. / Hakansson, M. / Walse, B. / Nilsson, C.L.
History
DepositionDec 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9837
Polymers41,4251
Non-polymers5576
Water4,252236
1
A: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules

A: Branched-chain-amino-acid aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,96514
Polymers82,8502
Non-polymers1,11512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area8080 Å2
ΔGint6 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.032, 84.032, 105.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 41425.062 Da / Num. of mol.: 1 / Mutation: T159R
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
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.2 M Sodiumfluoride, 0.1 M Bis Tris propane pH 6.5, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→28 Å / Num. obs: 57390 / % possible obs: 99.7 % / Redundancy: 9.7 % / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.6→27.52 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.771 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17939 2912 5.1 %RANDOM
Rwork0.1279 ---
obs0.13052 54393 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.2 Å20 Å2
2--0.2 Å20 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.6→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 35 236 3172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193123
X-RAY DIFFRACTIONr_bond_other_d0.0010.023036
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9754250
X-RAY DIFFRACTIONr_angle_other_deg0.87536984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8223.066137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27515533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1561525
X-RAY DIFFRACTIONr_chiral_restr0.1160.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213516
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02736
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5132.4111503
X-RAY DIFFRACTIONr_mcbond_other4.4972.411502
X-RAY DIFFRACTIONr_mcangle_it5.2983.6311890
X-RAY DIFFRACTIONr_mcangle_other5.3053.6321891
X-RAY DIFFRACTIONr_scbond_it6.8173.0341615
X-RAY DIFFRACTIONr_scbond_other6.8163.0351615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0254.312350
X-RAY DIFFRACTIONr_long_range_B_refined7.22821.1483544
X-RAY DIFFRACTIONr_long_range_B_other7.22821.1523545
X-RAY DIFFRACTIONr_rigid_bond_restr6.29836152
X-RAY DIFFRACTIONr_sphericity_free29.486579
X-RAY DIFFRACTIONr_sphericity_bonded17.96556229
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 196 -
Rwork0.248 3806 -
obs--95.7 %

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