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- PDB-9j0v: Crystal structure of monomeric PLP-dependent transaminase from De... -

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Basic information

Entry
Database: PDB / ID: 9j0v
TitleCrystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in P 21 21 21 space group
ComponentsDat: predicted D-alanine aminotransferase
KeywordsTRANSFERASE / DAAT / D-amino acid transaminase / TA / monomeric TA
Function / homology
Function and homology information


D-alanine-2-oxoglutarate aminotransferase activity / D-amino-acid transaminase / carboxylic acid biosynthetic process / cytosol
Similarity search - Function
Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / 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
DI(HYDROXYETHYL)ETHER / Dat: predicted D-alanine aminotransferase
Similarity search - Component
Biological speciesDesulfobacula toluolica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsMatyuta, I.O. / Bakunova, A.K. / Nikolaeva, A.Y. / Rakitina, T.V. / Bezsudnova, E.Y. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2024
Title: From Structure to Function: Analysis of the First Monomeric Pyridoxal-5'-Phosphate-Dependent Transaminase from the Bacterium Desulfobacula toluolica .
Authors: Bakunova, A.K. / Matyuta, I.O. / Nikolaeva, A.Y. / Rakitina, T.V. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionAug 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Jan 22, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dat: predicted D-alanine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4843
Polymers32,2851
Non-polymers1982
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-0 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.847, 56.226, 118.625
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 Dat: predicted D-alanine aminotransferase


Mass: 32285.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfobacula toluolica (bacteria) / Gene: dat, TOL2_C39420 / Production host: Escherichia coli (E. coli) / References: UniProt: K0NPP0, D-amino-acid transaminase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1M Ammonium acetate, 0.1M Bis-tris pH 5.5, 17% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.79→40.81 Å / Num. obs: 24352 / % possible obs: 98.8 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.028 / Rrim(I) all: 0.056 / Χ2: 0.97 / Net I/σ(I): 13.4 / Num. measured all: 88078
Reflection shellResolution: 1.79→1.83 Å / % possible obs: 96.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.67 / Num. measured all: 4831 / Num. unique obs: 1401 / CC1/2: 0.686 / Rpim(I) all: 0.405 / Rrim(I) all: 0.787 / Χ2: 0.83 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→40.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.205 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23575 1146 4.7 %RANDOM
Rwork0.19325 ---
obs0.19522 23150 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.029 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0 Å2
2---0.8 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.79→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 28 98 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131933
X-RAY DIFFRACTIONr_bond_other_d0.0030.0151872
X-RAY DIFFRACTIONr_angle_refined_deg2.11.6382614
X-RAY DIFFRACTIONr_angle_other_deg1.5011.574292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3665245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65321.79889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41315333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1551513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022158
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02424
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_it4.7763.872983
X-RAY DIFFRACTIONr_mcbond_other4.7793.869982
X-RAY DIFFRACTIONr_mcangle_it6.1485.7921227
X-RAY DIFFRACTIONr_mcangle_other6.1465.7961228
X-RAY DIFFRACTIONr_scbond_it5.8924.317950
X-RAY DIFFRACTIONr_scbond_other5.8894.32951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9536.2521388
X-RAY DIFFRACTIONr_long_range_B_refined9.66446.0612095
X-RAY DIFFRACTIONr_long_range_B_other9.67745.9352075
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 87 -
Rwork0.345 1661 -
obs--97.93 %

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