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- PDB-3uzb: Crystal Structures of Branched-Chain Aminotransferase from Deinoc... -

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Basic information

Entry
Database: PDB / ID: 3uzb
TitleCrystal Structures of Branched-Chain Aminotransferase from Deinococcus radiodurans Complexes with alpha-Ketoisocaproate and L-Glutamate Suggest Its Radio-Resistance for Catalysis
ComponentsBranched-chain-amino-acid aminotransferase
KeywordsTRANSFERASE / BCAT / Amino-acid biosynthesis / Aminotransferase / Branched-chain amino acid biosynthesis / Pyridoxal phosphate / alpha-Ketoisocaproate
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 / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Branched-chain amino acid aminotransferase II / 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 II / 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
2-OXO-4-METHYLPENTANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, C.D. / Huang, Y.C. / Chuankhayan, P. / Hsieh, Y.C. / Huang, T.F. / Lin, C.H. / Guan, H.H. / Liu, M.Y. / Chang, W.C. / Chen, C.J.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Crystal Structures of Complexes of the Branched-Chain Aminotransferase from Deinococcus radiodurans with alpha-Ketoisocaproate and L-Glutamate Suggest the Radiation Resistance of This Enzyme for Catalysis
Authors: Chen, C.D. / Lin, C.H. / Chuankhayan, P. / Huang, Y.C. / Hsieh, Y.C. / Huang, T.F. / Guan, H.H. / Liu, M.Y. / Chang, W.C. / Chen, C.J.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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


Theoretical massNumber of molelcules
Total (without water)159,37012
Polymers157,8614
Non-polymers1,5098
Water3,117173
1
A: Branched-chain-amino-acid aminotransferase
B: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6856
Polymers78,9312
Non-polymers7554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-16 kcal/mol
Surface area23860 Å2
MethodPISA
2
C: Branched-chain-amino-acid aminotransferase
D: Branched-chain-amino-acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6856
Polymers78,9312
Non-polymers7554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-15 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.110, 172.580, 80.080
Angle α, β, γ (deg.)90.00, 108.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39465.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_1626 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9RTX5, branched-chain-amino-acid transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.15M magnesium chloride, 15%(w/v) polyethylene glycol 8000, 0.1M Tris(pH 7.3), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 34610 / Num. obs: 29754 / % possible obs: 87.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.14 / Net I/σ(I): 8.85
Reflection shellResolution: 3→3.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.46 / Num. unique all: 3370 / Rsym value: 0.417 / % possible all: 87.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2COJ

2coj


Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 --RANDOM
Rwork0.204 ---
obs0.204 29754 92.7 %-
all-34610 --
Displacement parametersBiso mean: 24.6723 Å2
Baniso -1Baniso -2Baniso -3
1-2.021 Å20 Å2-8.018 Å2
2---5.509 Å20 Å2
3---3.488 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10420 0 96 173 10689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.375
LS refinement shellResolution: 3→3.06 Å / Rfactor Rfree error: 0.39
RfactorNum. reflection% reflection
Rfree0.271 3370 -
Rwork0.204 --
obs-3370 87.7 %

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