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

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Basic information

Entry
Database: PDB / ID: 8pnw
TitleCrystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in holo form with PLP
ComponentsBranched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
KeywordsTRANSFERASE / Aminotransferase / DAAT / PLP / transaminase
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
PYRIDOXAL-5'-PHOSPHATE / Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase
Similarity search - Component
Biological speciesBlastococcus saxobsidens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Dec 13, 2023Group: Database references / Category: citation / citation_author

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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)29,3023
Polymers29,0191
Non-polymers2832
Water5,495305
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)58,6036
Polymers58,0382
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5930 Å2
ΔGint-53 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.935, 105.935, 51.324
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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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-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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.86 Å3/Da / Density % sol: 57.07 %
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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.7→52.97 Å / Num. obs: 35723 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.051 / Rrim(I) all: 0.098 / Χ2: 0.95 / Net I/σ(I): 10.1 / Num. measured all: 124016
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 91.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.481 / Num. measured all: 4957 / Num. unique obs: 1760 / CC1/2: 0.792 / Rpim(I) all: 0.33 / Rrim(I) all: 0.586 / Χ2: 0.37 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→52.97 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.217 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19246 1700 4.8 %RANDOM
Rwork0.17094 ---
obs0.172 34008 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å2-0 Å2
2--0.54 Å20 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.7→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 16 305 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132125
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142035
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6372923
X-RAY DIFFRACTIONr_angle_other_deg1.4941.574656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56219.01101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.951522
X-RAY DIFFRACTIONr_chiral_restr0.0880.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02484
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_it1.8212.2091121
X-RAY DIFFRACTIONr_mcbond_other1.8182.2081120
X-RAY DIFFRACTIONr_mcangle_it2.5973.311402
X-RAY DIFFRACTIONr_mcangle_other2.5973.311403
X-RAY DIFFRACTIONr_scbond_it2.7982.4311004
X-RAY DIFFRACTIONr_scbond_other2.8022.4331001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0953.5611517
X-RAY DIFFRACTIONr_long_range_B_refined5.06127.5942402
X-RAY DIFFRACTIONr_long_range_B_other4.9626.9082325
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
Rfree0.292 110 -
Rwork0.269 2337 -
obs--91.68 %

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