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

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Basic information

Entry
Database: PDB / ID: 8yrv
TitleCrystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis complexed with 3-aminooxypropionic acid
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / complex / transaminase / aminotransferase / D-amino acid / 3-aminooxypropionic acid / oxyme
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
Chem-OCF / branched-chain-amino-acid transaminase
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis DSM 1100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMatyuta, I.O. / Bakunova, A.K. / Nikolaeva, A.Y. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Naturae / Year: 2024
Title: Insights into the Functioning of the D-amino Acid Transaminase from Haliscomenobacter Hydrossis via a Structural and Spectral Analysis of its Complex with 3-Aminooxypropionic Acid.
Authors: Bakunova, A.K. / Matyuta, I.O. / Nikolaeva, A.Y. / Boyko, K.M. / Khomutov, A.R. / Bezsudnova, E.Y. / Popov, V.O.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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)32,6803
Polymers32,3221
Non-polymers3592
Water5,531307
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3616
Polymers64,6442
Non-polymers7174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area4730 Å2
ΔGint-21 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.772, 71.232, 52.549
Angle α, β, γ (deg.)90.00, 101.26, 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-OCF / 3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid / PYRIDOXAMINE-5'-PHOSPHATE linked to 3-aminooxypropionic acid


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#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.: 307 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2M MgCl2, 0.1M Bis-tris pH 5.5, 25% PEG 3350, 6mM PLP, 12mM 3-aminooxypropionic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.74503 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.74503 Å / Relative weight: 1
ReflectionResolution: 1.7→35.34 Å / Num. obs: 32789 / % possible obs: 94.9 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.054 / Rrim(I) all: 0.1 / Χ2: 1.01 / Net I/σ(I): 11.4 / Num. measured all: 107399
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.484 / Num. measured all: 6072 / Num. unique obs: 1795 / CC1/2: 0.602 / Rpim(I) all: 0.312 / Rrim(I) all: 0.578 / Χ2: 0.52 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.8data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.51 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 1667 5.1 %RANDOM
Rwork0.16569 ---
obs0.16793 31120 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0.28 Å2
2--0.2 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.7→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 23 307 2556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132352
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152239
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6493189
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5765125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9855287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38921.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36315401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0471522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
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_it1.441.5161126
X-RAY DIFFRACTIONr_mcbond_other1.4391.5141123
X-RAY DIFFRACTIONr_mcangle_it2.1282.2621405
X-RAY DIFFRACTIONr_mcangle_other2.1282.2621405
X-RAY DIFFRACTIONr_scbond_it2.151.7751226
X-RAY DIFFRACTIONr_scbond_other2.1291.7711221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3412.571780
X-RAY DIFFRACTIONr_long_range_B_refined4.96819.2082807
X-RAY DIFFRACTIONr_long_range_B_other4.77718.6852735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 133 -
Rwork0.257 2363 -
obs--98.58 %

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