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

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Basic information

Entry
Database: PDB / ID: 7nea
TitleCrystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M3 mutant).
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / transaminase / aminotransferase / BCAT / IV-fold type / PLP-dependent enzymes / branched-chain amino acid aminotransferases
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 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)36,8989
Polymers36,3831
Non-polymers5158
Water4,792266
1
A: Branched-chain-amino-acid aminotransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)221,38654
Polymers218,2996
Non-polymers3,08748
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area34010 Å2
ΔGint-405 kcal/mol
Surface area60470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.497, 146.497, 143.776
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21A-744-

HOH

31A-754-

HOH

41A-763-

HOH

51A-764-

HOH

61A-765-

HOH

71A-766-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36383.184 Da / Num. of mol.: 1 / Mutation: G40V, R42S, Y100F
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

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Non-polymers , 5 types, 274 molecules

#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

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

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: 1.75→95.13 Å / Num. obs: 58749 / % possible obs: 98.6 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Net I/σ(I): 11.3 / Num. measured all: 166757 / Scaling rejects: 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
1.75-1.782.80.897887132000.4010.6231.102198.2
9.09-95.132.60.01511724440.9990.010.01847.995.2

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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: 6GKR

6gkr


Resolution: 2→95.13 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.718 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1991 5 %RANDOM
Rwork0.1614 ---
obs0.1634 37506 98.51 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.57 Å2 / Biso mean: 31.195 Å2 / Biso min: 12.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 2→95.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 27 267 2775
Biso mean--45.83 38.86 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172407
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.6493578
X-RAY DIFFRACTIONr_angle_other_deg1.5331.5715513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6275312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.39520.184163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7741529
X-RAY DIFFRACTIONr_chiral_restr0.1130.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023192
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02665
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 143 -
Rwork0.198 2755 -
all-2898 -
obs--99.08 %
Refinement TLS params.Method: refined / Origin x: 7.4361 Å / Origin y: 24.1403 Å / Origin z: 16.4951 Å
111213212223313233
T0.0306 Å2-0.0002 Å2-0.018 Å2-0.0479 Å2-0.011 Å2--0.0247 Å2
L0.8718 °20.4246 °20.2867 °2-0.4811 °20.0641 °2--0.4234 °2
S-0.0174 Å °-0.1672 Å °0.0304 Å °0.0376 Å °-0.0543 Å °0.0093 Å °-0.0209 Å °-0.112 Å °0.0717 Å °

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