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- PDB-6gkr: Crystal structure of branched-chain amino acid aminotransferase f... -

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Basic information

Entry
Database: PDB / ID: 6gkr
TitleCrystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum in PLP-form (holo-form)
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / branched-chain / aminotransferase / PLP / PMP / transaminase / thermophlic / dimer / Thermobaculum terrenum
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 / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesThermobaculum terrenum ATCC BAA-798 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsBoyko, K.M. / Bezsudnova, E.Y. / Nikolaeva, A.Y. / Zeifman, Y.S. / Rakitina, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
CitationJournal: Biochimie / Year: 2018
Title: Biochemical and structural insights into PLP fold type IV transaminase from Thermobaculum terrenum.
Authors: Bezsudnova, E.Y. / Boyko, K.M. / Nikolaeva, A.Y. / Zeifman, Y.S. / Rakitina, T.V. / Suplatov, D.A. / Popov, V.O.
History
DepositionMay 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Refinement description / Category: software / Item: _software.version
Revision 1.2Jan 16, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Branched-chain-amino-acid aminotransferase
B: Branched-chain-amino-acid aminotransferase
C: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1539
Polymers109,2823
Non-polymers8716
Water8,737485
1
A: Branched-chain-amino-acid aminotransferase
B: Branched-chain-amino-acid aminotransferase
C: Branched-chain-amino-acid aminotransferase
hetero molecules

A: Branched-chain-amino-acid aminotransferase
B: Branched-chain-amino-acid aminotransferase
C: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,30618
Polymers218,5636
Non-polymers1,74312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area29650 Å2
ΔGint-176 kcal/mol
Surface area58200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.509, 146.610, 119.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

21B-649-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 6 - 310 / Label seq-ID: 5 - 309

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 36427.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobaculum terrenum ATCC BAA-798 (bacteria)
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.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.5 / Details: HEPES 0.1M pH 7.5; Sodium chloride 3.4M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→84.01 Å / Num. obs: 45692 / % possible obs: 98.3 % / Redundancy: 4.4 % / CC1/2: 0.99 / Rrim(I) all: 0.172 / Net I/σ(I): 7
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 4.2 % / CC1/2: 0.661 / Rrim(I) all: 0.884 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
MOLREPphasing
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GKP

6gkp
PDB Unreleased entry


Resolution: 2.19→84.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.529 / SU ML: 0.158 / SU R Cruickshank DPI: 0.2992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.198 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 2301 5 %RANDOM
Rwork0.1593 ---
obs0.1617 43383 98.01 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 135.76 Å2 / Biso mean: 30.27 Å2 / Biso min: 14.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2--1.93 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: final / Resolution: 2.19→84.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7398 0 51 485 7934
Biso mean--31.68 31.53 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127696
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.65110457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.88820.063477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.162151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9961587
X-RAY DIFFRACTIONr_chiral_restr0.1130.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025889
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A10103
12B10103
21A10079
22C10079
31B10066
32C10066
LS refinement shellResolution: 2.19→2.247 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 181 -
Rwork0.243 3160 -
all-3341 -
obs--98.88 %

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