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

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Basic information

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


aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / cytosol
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
NITRATE ION / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Chem-PW0 / Aminotransferase class IV
Similarity search - Component
Biological speciesAminobacterium colombiense (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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: To Be Published
Title: Probing of the structural and catalytic roles of the residues in the active site of transaminase from Aminobacterium colombiense
Authors: Shilova, S.A. / Khrenova, M.G. / Matyuta, I.O. / Nikolaeva, A.Y. / Klyachko, N.L. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionApr 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,20613
Polymers61,8382
Non-polymers1,36911
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-6 kcal/mol
Surface area21750 Å2
Unit cell
Length a, b, c (Å)61.400, 89.435, 101.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 338 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PW0 / (~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid


Mass: 376.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N2O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M NaNitrate, 0.1M Bis-tris propane pH 6.5, 20% PEG3350

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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: Jul 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.85→19.76 Å / Num. obs: 48141 / % possible obs: 99.6 % / Redundancy: 11.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.035 / Rrim(I) all: 0.119 / Χ2: 0.97 / Net I/σ(I): 15.9 / Num. measured all: 560284
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 99 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.997 / Num. measured all: 35180 / Num. unique obs: 2886 / CC1/2: 0.832 / Rpim(I) all: 0.295 / Rrim(I) all: 1.041 / Χ2: 1 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACT4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.947 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25006 2333 4.9 %RANDOM
Rwork0.19548 ---
obs0.19803 45644 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0 Å2
2--0.25 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.85→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 89 327 4705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134528
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154373
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6546132
X-RAY DIFFRACTIONr_angle_other_deg1.3761.56910108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2821.204216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44615797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9581532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
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_it2.0412.142208
X-RAY DIFFRACTIONr_mcbond_other2.0372.142207
X-RAY DIFFRACTIONr_mcangle_it2.943.2032758
X-RAY DIFFRACTIONr_mcangle_other2.943.2032759
X-RAY DIFFRACTIONr_scbond_it2.8492.3872320
X-RAY DIFFRACTIONr_scbond_other2.8542.3912311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1443.4673364
X-RAY DIFFRACTIONr_long_range_B_refined5.48526.1465106
X-RAY DIFFRACTIONr_long_range_B_other5.48526.1445107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8471 / 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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 152 -
Rwork0.311 3286 -
obs--98.31 %

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