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- PDB-8rai: Crystal structure of D-amino acid transaminase from Haliscomenoba... -

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Basic information

Entry
Database: PDB / ID: 8rai
TitleCrystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis point mutant R90I complexed with phenylhydrazine
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / point mutant / aminotransferase / transaminase / Haliscomenobacter hydrossis / phenylhydrazine / complex
Function / homology
Function and homology information


carboxylic acid biosynthetic process / organonitrogen compound biosynthetic process / transaminase activity
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
Chem-ZXN / Aminotransferase class IV
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis DSM 1100 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMatyuta, I.O. / Bakunova, A.K. / Minyaev, M.E. / Popov, V.O. / Bezsudnova, E.Y. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-74-30004 Russian Federation
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Multifunctionality of arginine residues in the active sites of non-canonical d-amino acid transaminases.
Authors: Bakunova, A.K. / Matyuta, I.O. / Minyaev, M.E. / Isaikina, T.Y. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 8, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7073
Polymers32,2781
Non-polymers4292
Water3,693205
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4146
Polymers64,5562
Non-polymers8594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4610 Å2
ΔGint-19 kcal/mol
Surface area22220 Å2
Unit cell
Length a, b, c (Å)85.749, 72.750, 52.341
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aminotransferase class IV


Mass: 32277.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliscomenobacter hydrossis DSM 1100 (bacteria)
Gene: Halhy_2446 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KWH0
#2: Chemical ChemComp-ZXN / [6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen phosphate


Mass: 337.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N3O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 45% (v/v) Tacsimate, 50 mM BISTRIS buffer, pH 7.0

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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: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→20.82 Å / Num. obs: 21415 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 0.96 / Net I/σ(I): 23 / Num. measured all: 141122
Reflection shellResolution: 2→2.05 Å / % possible obs: 96.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.281 / Num. measured all: 10310 / Num. unique obs: 1528 / CC1/2: 0.962 / Rpim(I) all: 0.117 / Rrim(I) all: 0.304 / Χ2: 1.11 / Net I/σ(I) obs: 7.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.82 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.538 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19626 1117 5.2 %RANDOM
Rwork0.15577 ---
obs0.15801 20275 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.061 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.91 Å2
2--0.11 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 2→20.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 29 205 2498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152309
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6493297
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5765286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2120.952147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2215414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1721524
X-RAY DIFFRACTIONr_chiral_restr0.080.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
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_it1.7621.8941147
X-RAY DIFFRACTIONr_mcbond_other1.7571.8921146
X-RAY DIFFRACTIONr_mcangle_it2.5112.8251437
X-RAY DIFFRACTIONr_mcangle_other2.5112.8271438
X-RAY DIFFRACTIONr_scbond_it2.5642.2651275
X-RAY DIFFRACTIONr_scbond_other2.5652.2661276
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9333.2871851
X-RAY DIFFRACTIONr_long_range_B_refined5.43923.2962816
X-RAY DIFFRACTIONr_long_range_B_other5.38622.9932773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 81 -
Rwork0.182 1457 -
obs--99.29 %

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