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

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Basic information

Entry
Database: PDB / ID: 8aie
TitleCrystal structure of D-amino acid aminotransferase from Aminobacterium colombiense complexed with D-cycloserine
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / Transaminase / DAAT / aminotransferase / complex / cycloserine / ketimine
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
Chem-LCS / Chem-M7L / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aminotransferase class IV
Similarity search - Component
Biological speciesAminobacterium colombiense (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shilova, S.A. / Popov, V.O. / Bezsudnova, E.Y.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Crystallography Reports / Year: 2023
Title: 3D Structure of D-Аmino Acid Тransaminase from Aminobacterium colombiense in Complex with D-Cycloserine
Authors: Shilova, S.A. / Matyuta, I.O. / Bezsudnova, E.Y. / Minyaev, M.E. / Nikolaeva, A.Y. / Popov, V.O. / Boyko, K.M.
History
DepositionJul 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
Revision 1.2Mar 6, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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)63,1306
Polymers61,9542
Non-polymers1,1774
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-24 kcal/mol
Surface area21590 Å2
Unit cell
Length a, b, c (Å)61.968, 90.028, 100.290
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: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 274 / Label seq-ID: 3 - 276

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-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
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-M7L / 3-azanyloxy-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic acid


Mass: 349.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2M NaNitrate, 0.1M Bis-tris propane pH 6,5, 20% PEG3350

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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: Jun 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.9→21.15 Å / Num. obs: 44377 / % possible obs: 98.9 % / Redundancy: 9.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.057 / Rrim(I) all: 0.178 / Net I/σ(I): 13.9 / Num. measured all: 422464
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
1.9-1.947.93.4832207327820.4171.2583.7150.594.7
8.91-21.154.60.02820904530.9980.0140.03256.490.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AHR

8ahr


Resolution: 1.9→21.15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2127 / WRfactor Rwork: 0.1739 / FOM work R set: 0.718 / SU B: 6.007 / SU ML: 0.158 / SU R Cruickshank DPI: 0.1905 / SU Rfree: 0.1713 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 2191 5 %RANDOM
Rwork0.219 ---
obs0.2212 41909 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.24 Å2 / Biso mean: 30.653 Å2 / Biso min: 14.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.9→21.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 77 239 4611
Biso mean--28.55 34.54 -
Num. residues----551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134515
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154312
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.6536134
X-RAY DIFFRACTIONr_angle_other_deg1.3881.5689955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16721.111225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90615782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8491533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02967
Refine LS restraints NCS

Ens-ID: 1 / Number: 8547 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 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
Rfree0.381 157 -
Rwork0.363 2911 -
all-3068 -
obs--94.05 %

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