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- PDB-8ahr: Crystal structure of D-amino acid aminotransferase from Aminobact... -

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Basic information

Entry
Database: PDB / ID: 8ahr
TitleCrystal structure of D-amino acid aminotransferase from Aminobacterium colombiense in holo form with PLP
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / Transaminase / DAAT / aminotransferase
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transaminase activity / amino acid biosynthetic process
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 speciesAminobacterium colombiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shilova, S.A. / Rakitina, T.V. / Popov, V.O. / Bezsudnova, E.Y.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: 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.
History
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase class IV
B: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4484
Polymers61,9542
Non-polymers4942
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.190, 80.974, 98.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: -1 - 275 / Label seq-ID: 1 - 277

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aminotransferase class IV


Mass: 30976.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aminobacterium colombiense (bacteria) / Strain: DSM 12261 / ALA-1 / Gene: Amico_1844 / Production host: Escherichia coli (E. coli) / References: UniProt: D5EHC5
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium nitrate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→43.78 Å / Num. obs: 38455 / % possible obs: 98.1 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.047 / Rrim(I) all: 0.094 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9440.754989624890.6140.420.871.999.3
9.11-43.773.70.0312943540.9990.0170.03533.489

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MQZ

5mqz


Resolution: 1.9→43.78 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2361 / WRfactor Rwork: 0.1799 / FOM work R set: 0.7506 / SU B: 5.491 / SU ML: 0.15 / SU R Cruickshank DPI: 0.1898 / SU Rfree: 0.1725 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1783 4.9 %RANDOM
Rwork0.1894 ---
obs0.1921 34694 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.99 Å2 / Biso mean: 32.811 Å2 / Biso min: 19.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å2-0 Å2-0 Å2
2--3.8 Å20 Å2
3----1.72 Å2
Refinement stepCycle: final / Resolution: 1.9→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 30 147 4366
Biso mean--29.48 35.7 -
Num. residues----542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134330
X-RAY DIFFRACTIONr_bond_other_d0.0050.0154146
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.6465885
X-RAY DIFFRACTIONr_angle_other_deg1.3871.5649572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0135545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72821.128195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14715739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6751529
X-RAY DIFFRACTIONr_chiral_restr0.1090.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024788
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02921
Refine LS restraints NCS

Ens-ID: 1 / Number: 8170 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 115 -
Rwork0.354 2508 -
all-2623 -
obs--91.94 %

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