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- PDB-5ofy: Crystal structure of the D183N variant of human Alanine:Glyoxylat... -

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Basic information

Entry
Database: PDB / ID: 5ofy
TitleCrystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at pH 9.0. 2.8 Ang; internal aldimine with PLP in the active site
ComponentsSerine--pyruvate aminotransferase
KeywordsTRANSFERASE / AMINOTRANSFERASE / DETOXIFICATION / LIVER
Function / homology
Function and homology information


oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glyoxylate metabolic process / L-alanine catabolic process / glycine biosynthetic process, by transamination of glyoxylate / L-serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / Glyoxylate metabolism and glycine degradation / glyoxylate catabolic process ...oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glyoxylate metabolic process / L-alanine catabolic process / glycine biosynthetic process, by transamination of glyoxylate / L-serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / Glyoxylate metabolism and glycine degradation / glyoxylate catabolic process / L-serine metabolic process / L-cysteine catabolic process / transaminase activity / amino acid binding / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / pyridoxal phosphate binding / peroxisome / intracellular membrane-bounded organelle / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / 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 ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / 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
1,4-DIETHYLENE DIOXIDE / PYRIDOXAL-5'-PHOSPHATE / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsGiardina, G. / Cutruzzola, F. / Borri Voltattorni, C. / Cellini, B. / Montioli, R.
CitationJournal: Sci Rep / Year: 2017
Title: Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis.
Authors: Giardina, G. / Paiardini, A. / Montioli, R. / Cellini, B. / Voltattorni, C.B. / Cutruzzola, F.
History
DepositionJul 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3973
Polymers43,0621
Non-polymers3352
Water52229
1
A: Serine--pyruvate aminotransferase
hetero molecules

A: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7946
Polymers86,1242
Non-polymers6704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9290 Å2
ΔGint-45 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.049, 89.049, 140.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

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Components

#1: Protein Serine--pyruvate aminotransferase / SPT / Alanine--glyoxylate aminotransferase / AGT


Mass: 43061.852 Da / Num. of mol.: 1 / Mutation: D183N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Production host: Escherichia coli (E. coli)
References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9
Details: protein - 15 mg/ml (165 microM) in 40 mM PhO pH 7.4, 60 mM Hepes pH 7.0, 1.6 molar excess PLP Reservoir - Hampton Research Crystal Screen solution H12 - 2% dioxane, 0.1M bicine pH 9.0, 10% ...Details: protein - 15 mg/ml (165 microM) in 40 mM PhO pH 7.4, 60 mM Hepes pH 7.0, 1.6 molar excess PLP Reservoir - Hampton Research Crystal Screen solution H12 - 2% dioxane, 0.1M bicine pH 9.0, 10% PEG 20K Mixing - 0.4 + 0.4 microL
PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→46.95 Å / Num. obs: 14614 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.026 / Rrim(I) all: 0.091 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.9512.11.0322.50.9580.3081.07899.8
8.85-46.9511.30.040.9990.0120.04299.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.512
Highest resolutionLowest resolution
Rotation46.94 Å3.07 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
Aimless0.5.31data scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LUC

5luc


Resolution: 2.8→46 Å / SU B: 26.913 / SU ML: 0.456 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.923 / ESU R Free: 0.429 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.324 684 4.7 %RANDOM
Rwork0.262 ---
obs0.265 13721 98.8 %-
Displacement parametersBiso mean: 89.86 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å20 Å20 Å2
2--4.99 Å20 Å2
3----9.99 Å2
Refinement stepCycle: 1 / Resolution: 2.8→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 6 29 2947

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