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- PDB-7neb: Crystal structure of branched-chain amino acid aminotransferase f... -

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Basic information

Entry
Database: PDB / ID: 7neb
TitleCrystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M4 mutant)
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / transaminase / aminotransferase / BCAT / IV-fold type / PLP-dependent enzymes / branched-chain amino acid aminotransferases / mutant
Function / homology
Function and homology information


L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Branched-chain amino acid aminotransferase I / 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
PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesThermobaculum terrenum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsBoyko, K.M. / Petrova, T. / Nikolaeva, A.Y. / Zeifman, Y.S. / Rakitina, T.V. / Suplatov, D.A. / Popov, V.O. / Bezsudnova, E.Y.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Plos One / Year: 2021
Title: Probing the role of the residues in the active site of the transaminase from Thermobaculum terrenum.
Authors: Bezsudnova, E.Y. / Nikolaeva, A.Y. / Bakunova, A.K. / Rakitina, T.V. / Suplatov, D.A. / Popov, V.O. / Boyko, K.M.
History
DepositionFeb 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 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: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7233
Polymers36,4531
Non-polymers2702
Water2,108117
1
A: Branched-chain-amino-acid aminotransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)220,34118
Polymers218,7206
Non-polymers1,62112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area26930 Å2
ΔGint-153 kcal/mol
Surface area59760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.020, 146.020, 142.115
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Branched-chain-amino-acid aminotransferase / BCAT


Mass: 36453.297 Da / Num. of mol.: 1 / Mutation: G41V, R43S, Y101F, S115R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobaculum terrenum (strain ATCC BAA-798 / YNP1) (bacteria)
Strain: ATCC BAA-798 / YNP1 / Gene: ilvE, Tter_1720 / Production host: Escherichia coli (E. coli)
References: UniProt: D1CCW1, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4 Å3/Da
Crystal growTemperature: 293 K / Method: liquid diffusion / Details: HEPES 0.1M pH 7.5; Sodium chloride 3.4M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→94.47 Å / Num. obs: 45188 / % possible obs: 98.8 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.041 / Rrim(I) all: 0.083 / Net I/σ(I): 10 / Num. measured all: 178796 / Scaling rejects: 49
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
1.9-1.9443.8051158229100.1212.1894.4060.399.4
9.11-94.473.80.014165443510.0080.01781.696

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q8E

6q8e


Resolution: 2.2→94.47 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.526 / SU ML: 0.136 / SU R Cruickshank DPI: 0.1823 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1508 5.2 %RANDOM
Rwork0.2057 ---
obs0.2083 27662 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.5 Å2 / Biso mean: 48.664 Å2 / Biso min: 23.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å2-0 Å2
2--0.69 Å2-0 Å2
3----2.23 Å2
Refinement stepCycle: final / Resolution: 2.2→94.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 16 117 2566
Biso mean--62.02 48.09 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132603
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172395
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.6493558
X-RAY DIFFRACTIONr_angle_other_deg1.4711.5755501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1255322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02620.247162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24815428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5751529
X-RAY DIFFRACTIONr_chiral_restr0.1120.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023191
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02662
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 107 -
Rwork0.305 2044 -
all-2151 -
obs--99.26 %

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