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- PDB-1a3g: BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1a3g
TitleBRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE FROM ESCHERICHIA COLI
ComponentsBRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / PYRIDOXAL ENZYME
Function / homology
Function and homology information


aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / 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 ...aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / 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 / identical protein binding / cytosol
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
PYRIDOXAL-5'-PHOSPHATE / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.5 Å
AuthorsOkada, K. / Hirotsu, K. / Sato, M. / Hayashi, H. / Kagamiyama, H.
CitationJournal: J.Biochem.(Tokyo) / Year: 1997
Title: Three-dimensional structure of Escherichia coli branched-chain amino acid aminotransferase at 2.5 A resolution.
Authors: Okada, K. / Hirotsu, K. / Sato, M. / Hayashi, H. / Kagamiyama, H.
History
DepositionJan 21, 1998-
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7436
Polymers102,0013
Non-polymers7413
Water9,368520
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)205,48512
Polymers204,0026
Non-polymers1,4836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area27870 Å2
ΔGint-131 kcal/mol
Surface area55940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)135.100, 144.000, 102.900
Angle α, β, γ (deg.)90.00, 136.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE /


Mass: 34000.383 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0AB80, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 28% PEG 400, 200MM MGCL2, 100MM HEPES, PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMHEPES1reservoir
2200 mM1reservoirMgCl2
328 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 39622 / % possible obs: 83.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.059

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 2.5→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2044 10 %RANDOM
Rwork0.188 ---
obs0.188 37577 83.6 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6909 0 45 520 7474
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.351 170 2.91 %
Rwork0.325 3459 -
obs--59.28 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.PLPTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.325

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