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- PDB-7p8o: Crystal structure of D-aminoacid transaminase from Haliscomenobac... -

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Basic information

Entry
Database: PDB / ID: 7p8o
TitleCrystal structure of D-aminoacid transaminase from Haliscomenobacter hydrossis in its intermediate form
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / Transaminase / DATA / aminotransferase / apo
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity / metal ion binding
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
Aminotransferase class IV
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis DSM 1100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Bakunova, A.K. / Nikolaeva, A.Y. / Rakitina, T.V. / Bezsudnova, E.Y. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2024
Title: Incorporation of pyridoxal-5'-phosphate into the apoenzyme: A structural study of D-amino acid transaminase from Haliscomenobacter hydrossis.
Authors: Bakunova, A.K. / Matyuta, I.O. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022-
Revision 1.1Jan 31, 2024-
Revision 2.0Jul 3, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_conn / struct_sheet_range
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num ..._entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _reflns.pdbx_chi_squared / _reflns.pdbx_scaling_rejects / _struct_conn.pdbx_dist_value / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4423
Polymers32,3221
Non-polymers1202
Water1,51384
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8846
Polymers64,6442
Non-polymers2414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5490 Å2
ΔGint-85 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.636, 72.374, 51.822
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aminotransferase class IV


Mass: 32321.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliscomenobacter hydrossis DSM 1100 (bacteria)
Strain: ATCC 27775 / DSM 1100 / LMG 10767 / O / Gene: Halhy_2446 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KWH0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: MES 0.1 M pH 6.5; MgSO4; 1.8 M NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→51.03 Å / Num. obs: 22696 / % possible obs: 97.5 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.033 / Rrim(I) all: 0.059 / Χ2: 0.89 / Net I/σ(I): 10.9 / Num. measured all: 65244
Reflection shellResolution: 1.95→2 Å / % possible obs: 95.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.394 / Num. measured all: 4556 / Num. unique obs: 1541 / CC1/2: 0.885 / Rpim(I) all: 0.265 / Rrim(I) all: 0.476 / Χ2: 0.88 / Net I/σ(I) obs: 2.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CM0

5cm0


Resolution: 1.95→39.87 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.071 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23153 1105 4.9 %RANDOM
Rwork0.19115 ---
obs0.19323 21576 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-2.25 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.95→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 6 84 2253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.6362961
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7885266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84921.694124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05515358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4351517
X-RAY DIFFRACTIONr_chiral_restr0.1140.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021676
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_it3.0643.1541067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.1724.6981329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9823.5661114
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.5142.8973201
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 78 -
Rwork0.274 1556 -
obs--96.69 %

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