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- PDB-5ce8: Crystal structure of branched-chain aminotransferase from thermop... -

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Basic information

Entry
Database: PDB / ID: 5ce8
TitleCrystal structure of branched-chain aminotransferase from thermophilic archaea Thermoproteus uzoniensis
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 4, branched-chain amino acid transferase, N-terminal domain / 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 I / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesThermoproteus uzoniensis (archaea)
Thermoproteus uzoniensis 768-20 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Rakitin, A.L. / Ravin, N.V. / Popov, V.O.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Scientific Fund14-24-00172 Russian Federation
7th EU Frame Programme (ERA-IB)EIB.12.012
CitationJournal: Extremophiles / Year: 2016
Title: First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for L-amino acids and R-amines.
Authors: Boyko, K.M. / Stekhanova, T.N. / Nikolaeva, A.Y. / Mardanov, A.V. / Rakitin, A.L. / Ravin, N.V. / Bezsudnova, E.Y. / Popov, V.O.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)103,7287
Polymers102,8813
Non-polymers8484
Water5,999333
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)207,45714
Polymers205,7626
Non-polymers1,6958
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area29370 Å2
ΔGint-132 kcal/mol
Surface area51840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.540, 93.540, 212.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Branched-chain amino acid aminotransferase


Mass: 34293.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus uzoniensis (strain 768-20) (archaea)
Gene: TUZN_1299 / Production host: Escherichia coli (E. coli) / References: UniProt: F2L0W0
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P
Source: (gene. exp.) Thermoproteus uzoniensis 768-20 (archaea)
Gene: TUZN_1299 / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 5% w/v PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.491
11K, H, -L20.509
ReflectionResolution: 2→75.69 Å / Num. all: 72201 / Num. obs: 72105 / % possible obs: 99.87 % / Observed criterion σ(I): -3 / Redundancy: 19.6 % / Biso Wilson estimate: 32.901 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.123 / Χ2: 0.912 / Net I/σ(I): 19.28 / Num. measured all: 1413383
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.119.80.880.6794.77192859974097280.69799.9
2.1-2.20.9380.4976.8162326804580450.51100
2.2-2.40.9640.3599.6423511512443124250.36999.9
2.4-2.630.9860.23314.52204767996899680.239100
2.63-2.810.9910.17418.82114117570257010.178100
2.81-3.030.9940.13222.6197718525752380.13699.6
3.03-3.320.9960.09929.7298246498949880.102100
3.32-3.710.9970.08335.6888775448644860.086100
3.71-4.270.9970.06940.3173625394039280.07199.7
4.27-5.20.9980.06243.1463231335733410.06399.5
5.2-7.240.9980.05943.152702265826580.061100
7.24-800.9990.04845.8329902161515990.04999
801

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EIY

2eiy


Resolution: 2→75.69 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1635 / WRfactor Rwork: 0.1159 / FOM work R set: 0.8849 / SU B: 2.359 / SU ML: 0.067 / SU R Cruickshank DPI: 0.022 / SU Rfree: 0.0235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1681 3583 5 %RANDOM
Rwork0.1199 ---
obs0.1222 68521 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 73.81 Å2 / Biso mean: 26.434 Å2 / Biso min: 11.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å20 Å2
2--2.7 Å20 Å2
3----5.4 Å2
Refinement stepCycle: final / Resolution: 2→75.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6873 0 7 333 7213
Biso mean--23.79 29.03 -
Num. residues----887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0197016
X-RAY DIFFRACTIONr_bond_other_d0.0020.026845
X-RAY DIFFRACTIONr_angle_refined_deg2.3961.9889535
X-RAY DIFFRACTIONr_angle_other_deg1.263315679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7375884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8122.954281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8761559
X-RAY DIFFRACTIONr_chiral_restr0.1560.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217817
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021515
X-RAY DIFFRACTIONr_mcbond_it2.8562.5313545
X-RAY DIFFRACTIONr_mcbond_other2.8532.5313544
X-RAY DIFFRACTIONr_mcangle_it3.6943.7894426
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 236 -
Rwork0.208 5043 -
all-5279 -
obs--99.57 %

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