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

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Basic information

Entry
Database: PDB / ID: 8yru
TitleCrystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / apo form / transaminase / aminotransferase / D-amino acid
Function / homology
Function and homology information


carboxylic acid biosynthetic process / branched-chain-amino-acid transaminase / transaminase activity / amino acid biosynthetic process / 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
ACETATE ION / Chem-ZXN / branched-chain-amino-acid transaminase
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. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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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)32,7183
Polymers32,3221
Non-polymers3962
Water2,234124
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4366
Polymers64,6442
Non-polymers7934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3590 Å2
ΔGint-19 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 71.780, 52.241
Angle α, β, γ (deg.)90.00, 100.72, 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)
Gene: Halhy_2446 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KWH0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 45% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→21.43 Å / Num. obs: 21346 / % possible obs: 99 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.092 / Χ2: 0.95 / Net I/σ(I): 16.8 / Num. measured all: 119567
Reflection shellResolution: 2→2.05 Å / % possible obs: 89.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.546 / Num. measured all: 6358 / Num. unique obs: 1390 / CC1/2: 0.824 / Rpim(I) all: 0.276 / Rrim(I) all: 0.615 / Χ2: 0.91 / Net I/σ(I) obs: 2.8

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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→21.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.08 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23214 1071 5 %RANDOM
Rwork0.17656 ---
obs0.17928 20260 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-0.53 Å2
2---0.03 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2→21.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 27 124 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132244
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152110
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.6463045
X-RAY DIFFRACTIONr_angle_other_deg1.3781.5764822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.34520.992131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37915369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8021521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
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_it2.8272.7391089
X-RAY DIFFRACTIONr_mcbond_other2.8212.7371087
X-RAY DIFFRACTIONr_mcangle_it4.1064.0861358
X-RAY DIFFRACTIONr_mcangle_other4.1064.0881359
X-RAY DIFFRACTIONr_scbond_it3.5953.1861155
X-RAY DIFFRACTIONr_scbond_other3.5933.1851156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3934.6491686
X-RAY DIFFRACTIONr_long_range_B_refined7.36932.5862490
X-RAY DIFFRACTIONr_long_range_B_other7.34732.4912474
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
Rfree0.272 61 -
Rwork0.25 1332 -
obs--89.93 %

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