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- PDB-8onj: Crystal structure of D-amino acid aminotransferase from Aminobact... -

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Basic information

Entry
Database: PDB / ID: 8onj
TitleCrystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant R88L
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / Transaminase / point mutant / aminotransferase
Function / homology
Function and homology information


carboxylic acid biosynthetic process / organonitrogen compound biosynthetic process / transaminase activity
Similarity search - Function
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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase class IV
Similarity search - Component
Biological speciesAminobacterium colombiense (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Minyaev, M.E. / Shilova, S.A. / Bezsudnova, E.Y. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Biochem.J. / Year: 2023
Title: In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.
Authors: Shilova, S.A. / Matyuta, I.O. / Khrenova, M.G. / Nikolaeva, A.Y. / Klyachko, N.L. / Minyaev, M.E. / Khomutov, A.R. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionApr 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase class IV
B: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4665
Polymers61,8662
Non-polymers6003
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-24 kcal/mol
Surface area21110 Å2
Unit cell
Length a, b, c (Å)60.791, 88.553, 100.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminotransferase class IV


Mass: 30932.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aminobacterium colombiense (bacteria) / Gene: Amico_1844 / Production host: Escherichia coli (E. coli) / References: UniProt: D5EHC5
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→88.55 Å / Num. obs: 50878 / % possible obs: 99.6 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Χ2: 0.99 / Net I/σ(I): 14.3 / Num. measured all: 306052
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 95.8 % / Redundancy: 3 % / Rmerge(I) obs: 1.108 / Num. measured all: 8483 / Num. unique obs: 2853 / CC1/2: 0.389 / Rpim(I) all: 0.746 / Rrim(I) all: 1.345 / Χ2: 0.91 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PDB_EXTRACT4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→66.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.22 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2498 4.9 %RANDOM
Rwork0.18922 ---
obs0.19069 48313 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0 Å2
2--0.38 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.8→66.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 37 255 4501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154234
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.6476010
X-RAY DIFFRACTIONr_angle_other_deg1.5221.5649789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52421.498207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12815763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0481529
X-RAY DIFFRACTIONr_chiral_restr0.0880.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02939
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_it2.3952.4842191
X-RAY DIFFRACTIONr_mcbond_other2.3952.4842190
X-RAY DIFFRACTIONr_mcangle_it3.2573.7112736
X-RAY DIFFRACTIONr_mcangle_other3.2573.7112737
X-RAY DIFFRACTIONr_scbond_it3.2722.7692231
X-RAY DIFFRACTIONr_scbond_other3.2712.772232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8524.0323270
X-RAY DIFFRACTIONr_long_range_B_refined5.8329.6584879
X-RAY DIFFRACTIONr_long_range_B_other5.81529.5394849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8434 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 182 -
Rwork0.308 3375 -
obs--95.26 %

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