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- PDB-7p7x: Crystal structure of D-amino acid transaminase from Haliscomenoba... -

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Basic information

Entry
Database: PDB / ID: 7p7x
TitleCrystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form).
ComponentsAminotransferase class IV
KeywordsTRANSFERASE / transaminase / amino transferase / DAAT / D-amino acid / PLP
Function / homology
Function and homology information


aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / metal ion binding / cytosol
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
ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Aminotransferase class IV
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Bakunova, A.K. / Rakitina, T.V. / Bezsudnova, E.Y. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Molecules / Year: 2021
Title: The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis : Biochemical and Structural Insights into the New Enzyme.
Authors: Bakunova, A.K. / Nikolaeva, A.Y. / Rakitina, T.V. / Isaikina, T.Y. / Khrenova, M.G. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionJul 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 10, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,9794
Polymers34,5781
Non-polymers4013
Water3,081171
1
A: Aminotransferase class IV
hetero molecules

A: Aminotransferase class IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9598
Polymers69,1572
Non-polymers8026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5880 Å2
ΔGint-25 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.884, 71.752, 52.992
Angle α, β, γ (deg.)90.000, 100.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aminotransferase class IV


Mass: 34578.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliscomenobacter hydrossis (strain ATCC 27775 / DSM 1100 / LMG 10767 / O) (bacteria)
Strain: ATCC 27775 / DSM 1100 / LMG 10767 / O / Gene: Halhy_2446 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KWH0
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium acetate pH 4.8; 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / 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: 1.75→52.03 Å / Num. obs: 31622 / % possible obs: 98.1 % / Redundancy: 3.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.087 / Rrim(I) all: 0.157 / Net I/σ(I): 3.8 / Num. measured all: 96630 / Scaling rejects: 237
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
1.75-1.783.11.492537017260.4470.9921.80.898.6
9.09-52.032.90.0536922360.9880.0340.0639.795.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC7.1.013refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+25 / Resolution: 2→52.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.38 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 985 4.7 %RANDOM
Rwork0.1803 ---
obs0.1831 20186 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.96 Å2 / Biso mean: 26.227 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å2-3.02 Å2
2---1.53 Å2-0 Å2
3---1.98 Å2
Refinement stepCycle: final / Resolution: 2→52.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 31 171 2474
Biso mean--31.69 30.7 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132361
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172242
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.6473200
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5775133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.925280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19321.522138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51315403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7371520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 78 -
Rwork0.259 1488 -
all-1566 -
obs--98.24 %

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