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- PDB-6thq: Crystal structure of branched-chain aminotransferase from thermop... -

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Basic information

Entry
Database: PDB / ID: 6thq
TitleCrystal structure of branched-chain aminotransferase from thermophilic archaea Thermoproteus uzoniensis with norvaline
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / aminotransferase / branched-chain / PLP / BCAT
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
Similarity search - Function
Branched-chain amino acid aminotransferase I / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / 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 / 2-[O-PHOSPHONOPYRIDOXYL]-AMINO-PENTANOIC ACID / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesThermoproteus uzoniensis 768-20 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Bezsudnova, E.Y. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00164 Russian Federation
CitationJournal: Crystallography Reports / Year: 2020
Title: Three-Dimensional Structure of Branched-Chain Amino Acid Transaminase from Thermoproteus uzoniensis in Complex with L-Norvaline
Authors: Boyko, K.M. / Nikolaeva, A.Y. / Timofeev, V.I. / Popov, V.O. / Bezsudnova, E.Y.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)104,6679
Polymers102,8813
Non-polymers1,7866
Water3,225179
1
A: Branched-chain-amino-acid aminotransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)69,7786
Polymers68,5872
Non-polymers1,1914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-1/31
Buried area5870 Å2
ΔGint-44 kcal/mol
Surface area21180 Å2
MethodPISA
2
B: Branched-chain-amino-acid aminotransferase
C: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7786
Polymers68,5872
Non-polymers1,1914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-47 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.460, 93.460, 213.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA-1 - 29411 - 306
21GLYGLYBB-1 - 29411 - 306
12SERSERAA0 - 29412 - 306
22SERSERCC0 - 29412 - 306
13SERSERBB0 - 29412 - 306
23SERSERCC0 - 29412 - 306

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 34293.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus uzoniensis 768-20 (archaea)
Gene: ilvE, TUZN_1299 / Production host: Escherichia coli (E. coli)
References: UniProt: F2L0W0, 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
#3: Chemical ChemComp-PY5 / 2-[O-PHOSPHONOPYRIDOXYL]-AMINO-PENTANOIC ACID / VITAMIN B6 COMPLEXED WITH 2-AMINO-PENTANOIC ACID


Mass: 348.289 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H21N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate trihydrate, pH 4.6, 8% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.15→80.94 Å / Num. obs: 58111 / % possible obs: 99.7 % / Redundancy: 8.153 % / Biso Wilson estimate: 49.495 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.068 / Χ2: 0.987 / Net I/σ(I): 22.96 / Num. measured all: 473788 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.28.3091.1112.2637660.7611.18398.2
2.2-2.38.2360.7553.2767140.8670.80599.7
2.3-2.47.6890.5783.9556940.9020.61999.5
2.4-2.58.5450.4415.4747560.9490.46999.9
2.5-38.1790.20810.62155220.9880.22299.8
3-48.2040.05434.25124080.9990.05799.9
4-108.0550.02470.83861610.02599.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CE8

5ce8


Resolution: 2.15→80.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2226 / WRfactor Rwork: 0.1592 / FOM work R set: 0.7005 / SU B: 8.666 / SU ML: 0.197 / SU R Cruickshank DPI: 0.2039 / SU Rfree: 0.1925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 2979 5.1 %RANDOM
Rwork0.1871 ---
obs0.1895 55103 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.28 Å2 / Biso mean: 48.145 Å2 / Biso min: 24.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å2-0 Å2
3----2.5 Å2
Refinement stepCycle: final / Resolution: 2.15→80.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 114 179 7249
Biso mean--40.59 44.32 -
Num. residues----894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197261
X-RAY DIFFRACTIONr_angle_refined_deg2.1411.9959847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11322.676299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.491151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8481568
X-RAY DIFFRACTIONr_chiral_restr0.1330.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215392
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92070.07
12B92070.07
21A91360.07
22C91360.07
31B91830.08
32C91830.08
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 209 -
Rwork0.37 3969 -
all-4178 -
obs--98.14 %

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