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- PDB-8ahu: Crystal structure of D-amino acid aminotrensferase from Haliscome... -

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Basic information

Entry
Database: PDB / ID: 8ahu
TitleCrystal structure of D-amino acid aminotrensferase from Haliscomenobacter hydrossis complexed with D-cycloserine
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / Transaminase / DAAT / aminotransferase / complex / D-cycloserine
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-LCS / Aminotransferase class IV
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Bakunova, A.K. / Popov, V.O. / Bezsudnova, E.Y.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Biochemistry Mosc. / Year: 2023
Title: Mechanism of D-Cycloserine Inhibition of D-Amino Acid Transaminase from Haliscomenobacter hydrossis.
Authors: Bakunova, A.K. / Matyuta, I.O. / Nikolaeva, A.Y. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
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.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)32,7453
Polymers32,3221
Non-polymers4232
Water4,810267
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4906
Polymers64,6442
Non-polymers8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6240 Å2
ΔGint-17 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.902, 71.940, 53.089
Angle α, β, γ (deg.)90.000, 101.470, 90.000
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 (bacteria) / Strain: ATCC 27775 / DSM 1100 / LMG 10767 / O / Gene: Halhy_2446 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KWH0
#2: 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
#3: Chemical ChemComp-LCS / [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate


Mass: 331.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium acetate pH 4.8, 16-22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.41→42.58 Å / Num. obs: 61465 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 6.5 / Num. measured all: 394915 / Scaling rejects: 41
Reflection shell

Diffraction-ID: 1 / Redundancy: 6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.41-1.430.4331824430270.9460.1880.4730.699.9
7.72-42.580.03323513920.9920.0150.03723.698.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P7X

7p7x


Resolution: 1.41→42.58 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.274 / SU ML: 0.074 / SU R Cruickshank DPI: 0.0576 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 3002 4.9 %RANDOM
Rwork0.1717 ---
obs0.1732 58305 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.42 Å2 / Biso mean: 21.939 Å2 / Biso min: 12.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å2-2.12 Å2
2---0.54 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 1.41→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 35 267 2571
Biso mean--27.74 32.83 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132398
X-RAY DIFFRACTIONr_bond_other_d0.0030.0152286
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.6523260
X-RAY DIFFRACTIONr_angle_other_deg1.5291.5785247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0155296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00520.922141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0591521
X-RAY DIFFRACTIONr_chiral_restr0.110.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022729
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02584
LS refinement shellResolution: 1.41→1.447 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 184 -
Rwork0.311 4205 -
all-4389 -
obs--97.14 %
Refinement TLS params.Method: refined / Origin x: 25.7408 Å / Origin y: -0.1727 Å / Origin z: 15.2983 Å
111213212223313233
T0.0338 Å20.004 Å2-0.0179 Å2-0.0138 Å2-0.0054 Å2--0.0211 Å2
L0.4208 °2-0.3589 °20.1363 °2-0.3447 °2-0.2212 °2--0.371 °2
S0.0087 Å °0.0033 Å °0.0012 Å °0.0049 Å °0.0137 Å °0.003 Å °-0.0388 Å °-0.0258 Å °-0.0224 Å °

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