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- PDB-8pny: Crystal structure of D-amino acid aminotransferase from Blastococ... -

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Basic information

Entry
Database: PDB / ID: 8pny
TitleCrystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens complexed with phenylhydrazine and in its apo form
ComponentsBranched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
KeywordsTRANSFERASE / Aminotransferase / DAAT / apo form / transaminase / phenylhydrazine / complex
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity / lyase activity / cytosol
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-ZXN / Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
Similarity search - Component
Biological speciesBlastococcus saxobsidens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shilova, S.A. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
Citation
Journal: Int J Mol Sci / Year: 2023
Title: Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens.
Authors: Shilova, S.A. / Matyuta, I.O. / Petrova, E.S. / Nikolaeva, A.Y. / Rakitina, T.V. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
#1: Journal: Molecules / Year: 2023
Title: To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense.
Authors: Shilova, S.A. / Khrenova, M.G. / Matyuta, I.O. / Nikolaeva, A.Y. / Rakitina, T.V. / Klyachko, N.L. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
#2: Journal: Int J Mol Sci / Year: 2023
Title: Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens
Authors: Shilova, S.A. / Matyuta, I.O. / Petrova, E.S. / Nikolaeva, A.Y. / Rakitina, T.V. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionJul 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.0Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3562
Polymers29,0191
Non-polymers3371
Water4,071226
1
A: Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
hetero molecules

A: Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7124
Polymers58,0382
Non-polymers6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_553x-y,-y,-z-4/31
Buried area4460 Å2
ΔGint-33 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.644, 104.644, 51.541
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase


Mass: 29018.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastococcus saxobsidens (bacteria) / Gene: BLASA_4517 / Production host: Escherichia coli (E. coli) / References: UniProt: H6RQF3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.5, 4 M NaCl

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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 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→22.59 Å / Num. obs: 30251 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.062 / Rrim(I) all: 0.224 / Χ2: 0.97 / Net I/σ(I): 10.7 / Num. measured all: 389046
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 96.6 % / Redundancy: 12.8 % / Rmerge(I) obs: 1.52 / Num. measured all: 22104 / Num. unique obs: 1727 / CC1/2: 0.506 / Rpim(I) all: 0.437 / Rrim(I) all: 1.583 / Χ2: 1.1 / Net I/σ(I) obs: 1.9

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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: 1.8→22.59 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.562 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25406 1429 4.7 %RANDOM
Rwork0.20322 ---
obs0.20568 28796 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.585 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.8→22.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 23 226 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142052
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6362961
X-RAY DIFFRACTIONr_angle_other_deg1.4441.574696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28319.38197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79815291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1311520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
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_it1.6441.771140
X-RAY DIFFRACTIONr_mcbond_other1.6421.7691139
X-RAY DIFFRACTIONr_mcangle_it2.5752.6481428
X-RAY DIFFRACTIONr_mcangle_other2.5752.6481429
X-RAY DIFFRACTIONr_scbond_it1.9621.9371010
X-RAY DIFFRACTIONr_scbond_other1.9611.9381011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0782.8391528
X-RAY DIFFRACTIONr_long_range_B_refined4.94122.092394
X-RAY DIFFRACTIONr_long_range_B_other4.82221.7462339
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 99 -
Rwork0.321 2050 -
obs--96.54 %

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