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

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Basic information

Entry
Database: PDB / ID: 8onl
TitleCrystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / Transaminase / point mutant / aminotransferase
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity
Similarity search - Function
: / 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
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aminotransferase class IV
Similarity search - Component
Biological speciesAminobacterium colombiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)62,3324
Polymers61,8382
Non-polymers4942
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-25 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.429, 88.013, 99.772
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: 30918.793 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


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


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M NaNitrate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.74503 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.74503 Å / Relative weight: 1
ReflectionResolution: 1.9→44.97 Å / Num. obs: 43170 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.052 / Rrim(I) all: 0.122 / Χ2: 0.98 / Net I/σ(I): 10.4 / Num. measured all: 232841
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.69 / Num. measured all: 15179 / Num. unique obs: 2747 / CC1/2: 0.731 / Rpim(I) all: 0.321 / Rrim(I) all: 0.763 / Χ2: 0.9 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
XDSdata reduction
REFMACphasing
PDB_EXTRACT4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.497 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26317 2156 5 %RANDOM
Rwork0.21328 ---
obs0.21577 40996 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.428 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0 Å20 Å2
2--1.79 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.9→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 30 267 4504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134373
X-RAY DIFFRACTIONr_bond_other_d0.0020.0154205
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.6485937
X-RAY DIFFRACTIONr_angle_other_deg1.3121.5659711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17321.176204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25215761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0821531
X-RAY DIFFRACTIONr_chiral_restr0.0910.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024808
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02933
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_it2.6152.6972172
X-RAY DIFFRACTIONr_mcbond_other2.6152.6972171
X-RAY DIFFRACTIONr_mcangle_it3.7154.032708
X-RAY DIFFRACTIONr_mcangle_other3.7154.032709
X-RAY DIFFRACTIONr_scbond_it3.1352.942201
X-RAY DIFFRACTIONr_scbond_other3.1352.9412198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5314.3053230
X-RAY DIFFRACTIONr_long_range_B_refined5.9332.174862
X-RAY DIFFRACTIONr_long_range_B_other5.87432.0684811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8318 / 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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 154 -
Rwork0.361 3014 -
obs--99.91 %

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