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- PDB-9j0u: Crystal structure of monomeric PLP-dependent transaminase from De... -

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Basic information

Entry
Database: PDB / ID: 9j0u
TitleCrystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in F 41 3 2 space group
ComponentsDat: predicted D-alanine aminotransferase
KeywordsTRANSFERASE / DAAT / D-amino acid transaminase / PLP / 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
Dat: predicted D-alanine aminotransferase
Similarity search - Component
Biological speciesDesulfobacula toluolica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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 / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_refine_tls_group / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.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_refine_tls_group.end_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: Dat: predicted D-alanine aminotransferase


Theoretical massNumber of molelcules
Total (without water)32,2851
Polymers32,2851
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)250.089, 250.089, 250.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 5.08 Å3/Da / Density % sol: 75.8 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 400mM NaNitrate, 0.1M 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: SPring-8 / Beamline: BL41XU / Wavelength: 0.89999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89999 Å / Relative weight: 1
ReflectionResolution: 2.58→144.39 Å / Num. obs: 21699 / % possible obs: 100 % / Redundancy: 66.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.023 / Rrim(I) all: 0.192 / Χ2: 0.92 / Net I/σ(I): 17.3 / Num. measured all: 1452550
Reflection shellResolution: 2.58→2.69 Å / % possible obs: 100 % / Redundancy: 37.6 % / Rmerge(I) obs: 9.059 / Num. measured all: 97661 / Num. unique obs: 2594 / CC1/2: 0.446 / Rpim(I) all: 1.437 / Rrim(I) all: 9.174 / Χ2: 0.84 / Net I/σ(I) obs: 0.9

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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: 2.58→88.58 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 26.494 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25274 1096 5.1 %RANDOM
Rwork0.20912 ---
obs0.21116 20573 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.156 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.58→88.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 15 15 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0122291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.4741.6353094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1735285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08621.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.40515418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.331517
X-RAY DIFFRACTIONr_chiral_restr0.2930.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021689
X-RAY DIFFRACTIONr_gen_planes_other
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_it8.2287.0711143
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.13110.6011427
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.5537.461147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15.75295.8013308
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 87 -
Rwork0.393 1493 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -18.389 Å / Origin y: -45.5359 Å / Origin z: -65.285 Å
111213212223313233
T0.4224 Å20.0477 Å20.0183 Å2-0.1318 Å20.0475 Å2--0.2051 Å2
L0.4627 °20.055 °2-0.2281 °2-1.653 °2-0.5355 °2--0.3564 °2
S-0.1441 Å °0.1793 Å °0.1452 Å °0.2826 Å °0.3035 Å °-0.0574 Å °0.0446 Å °-0.174 Å °-0.1594 Å °

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