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- PDB-2bkw: Yeast alanine:glyoxylate aminotransferase YFL030w -

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Basic information

Entry
Database: PDB / ID: 2bkw
TitleYeast alanine:glyoxylate aminotransferase YFL030w
ComponentsALANINE-GLYOXYLATE AMINOTRANSFERASE 1
KeywordsTRANSFERASE / ANALINE-GLYOXYLATE AMINOTRANSFERASE / PYRIDOXAL-5-PHOSPHATE / SAD / GLYCOLATE PATHWAY
Function / homology
Function and homology information


alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / peroxisome / mitochondrion / cytosol
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / PYRIDOXAL-5'-PHOSPHATE / Alanine--glyoxylate aminotransferase 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 Å
AuthorsMeyer, P. / Liger, D. / Leulliot, N. / Quevillon-Cheruel, S. / Zhou, C.Z. / Borel, F. / Ferrer, J.L. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
CitationJournal: Biochimie / Year: 2005
Title: Crystal Structure and Confirmation of the Alanine:Glyoxylate Aminotransferase Activity of the Yfl030W Yeast Protein
Authors: Meyer, P. / Liger, D. / Leulliot, N. / Quevillon-Cheruel, S. / Zhou, C.Z. / Borel, F. / Ferrer, J.L. / Poupon, A. / Janin, J. / Van Tilbeurgh, H.
History
DepositionFeb 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALANINE-GLYOXYLATE AMINOTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6043
Polymers42,2831
Non-polymers3212
Water1,60389
1
A: ALANINE-GLYOXYLATE AMINOTRANSFERASE 1
hetero molecules

A: ALANINE-GLYOXYLATE AMINOTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2096
Polymers84,5672
Non-polymers6424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area5970 Å2
ΔGint-21.4 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.400, 57.400, 184.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

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Components

#1: Protein ALANINE-GLYOXYLATE AMINOTRANSFERASE 1


Mass: 42283.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL 5'-PHOSPHATE LINK TO A 201, GLYOXYLATE / Source: (gene. exp.) SACCHAROMYCES CEREVISIAE S288C (yeast) / Plasmid: PET9 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P43567, alanine-glyoxylate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE, GLYOXYLATE / Glyoxylic acid


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: ALLOWS THE BIOSYNTHESIS OF GLYCINE

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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: 2.07 Å3/Da / Density % sol: 38 %
Crystal growDetails: 0.2 M AMONIUM SULPHATE, 30% PEG MME 2000, 0.1 M SODIUM ACETATE, PH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9784
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.57→28 Å / Num. obs: 11595 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.5
Reflection shellResolution: 2.57→2.65 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.9 / % possible all: 92.2

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Processing

Software
NameVersionClassification
XDSdata reduction
CCP4data scaling
CNSphasing
RESOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.57→28 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: FIRST AND LAST TWO RESIDUES ARE ABSENT FROM THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 599 5 %RANDOM
Rwork0.1985 ---
obs0.1985 11593 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.8386 Å2 / ksol: 0.31765 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.348 Å2-2.742 Å20 Å2
2--2.348 Å20 Å2
3----4.697 Å2
Refinement stepCycle: LAST / Resolution: 2.57→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 20 89 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00702
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.33127
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.1712
X-RAY DIFFRACTIONc_scbond_it2.2412
X-RAY DIFFRACTIONc_scangle_it3.2622.5
LS refinement shellResolution: 2.57→2.65 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.225 35 5 %
Rwork0.174 767 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_LLP.PARAMPROTEIN_LLP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GLV.PARAMGLV.TOP

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