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

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Basic information

Entry
Database: PDB / ID: 8raf
TitleCrystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis point mutant R90I (holo form)
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / DAAT / point mutant / aminotransferase / transaminase / Haliscomenobacter hydrossis
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
PYRIDOXAL-5'-PHOSPHATE / 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

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Assembly

Deposited unit
A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5252
Polymers32,2781
Non-polymers2471
Water3,369187
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0504
Polymers64,5562
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5180 Å2
ΔGint-21 kcal/mol
Surface area22440 Å2
Unit cell
Length a, b, c (Å)85.392, 72.627, 52.244
Angle α, β, γ (deg.)90.00, 100.80, 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.47 Å3/Da / Density % sol: 50.1 %
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: Dec 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→21.77 Å / Num. obs: 21132 / % possible obs: 99.4 % / Redundancy: 6.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.069 / Rrim(I) all: 0.177 / Χ2: 0.9 / Net I/σ(I): 7 / Num. measured all: 135237
Reflection shellResolution: 2→2.05 Å / % possible obs: 95 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.388 / Num. measured all: 7667 / Num. unique obs: 1470 / CC1/2: 0.92 / Rpim(I) all: 0.184 / Rrim(I) all: 0.431 / Χ2: 0.68 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CrysalisProdata reduction
REFMACphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.77 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.901 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23634 1097 5.2 %RANDOM
Rwork0.19419 ---
obs0.19649 19891 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.528 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å2-0.92 Å2
2---0.76 Å2-0 Å2
3---2.31 Å2
Refinement stepCycle: 1 / Resolution: 2→21.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 15 187 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132347
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152226
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.6453191
X-RAY DIFFRACTIONr_angle_other_deg1.4111.5745097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3295286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31221.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40115397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1221519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
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_it1.2451.3681132
X-RAY DIFFRACTIONr_mcbond_other1.2411.3661131
X-RAY DIFFRACTIONr_mcangle_it1.882.0421416
X-RAY DIFFRACTIONr_mcangle_other1.882.0441417
X-RAY DIFFRACTIONr_scbond_it1.9081.6411215
X-RAY DIFFRACTIONr_scbond_other1.911.6431212
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0052.3761774
X-RAY DIFFRACTIONr_long_range_B_refined4.36116.862723
X-RAY DIFFRACTIONr_long_range_B_other4.28116.6682689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 75 -
Rwork0.219 1379 -
obs--94.72 %

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