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- PDB-5hhy: Structure of human Alanine:Glyoxylate Aminotransferase major alle... -

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Basic information

Entry
Database: PDB / ID: 5hhy
TitleStructure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) showing X-Ray induced reduction of PLP internal aldimine to 4'-deoxy-piridoxine-phosphate (PLR)
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
Chem-PLR / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsGiardina, G. / Cutruzzola, F. / Borri Voltattorni, C. / Cellini, B. / Montioli, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Oxalosis and Hyperoxaluria FoundationOHF2011 United Kingdom
European Community's Seventh Framework Programme FP7/2007-2013BioStruct-X project 6943 grant agreement n.283570
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
DepositionJan 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2524
Polymers84,7862
Non-polymers4662
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-52 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.479, 101.880, 131.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42393.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Plasmid: pTRCHis2A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.15 Å3/Da / Density % sol: 42.78 % / Description: yellow plates
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein solution; 0.2 M AGT, 18mM potassium phosphate pH7.4, 20mM Hepes pH 7.4, 5% Jeffamine (Hampton), 5mM sodium hydroxylamine. Reservoir; PEG 6k 12%, 100 mM MES pH 5.0. Mixing: 1+1 microL ...Details: Protein solution; 0.2 M AGT, 18mM potassium phosphate pH7.4, 20mM Hepes pH 7.4, 5% Jeffamine (Hampton), 5mM sodium hydroxylamine. Reservoir; PEG 6k 12%, 100 mM MES pH 5.0. Mixing: 1+1 microL Cryoprotectant; 25% MPD
PH range: 5.0 - 6.0

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: dataset referes to 112.5 degrees (frames 151-300)
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.04 Å / Num. obs: 77240 / % possible obs: 95.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.49 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.05 / Net I/σ(I): 9 / Num. measured all: 298106 / Scaling rejects: 165
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.7-1.733.60.6591.31370338120.6830.37490.3
9-48.044.20.03325.324925950.9970.01894.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H0C

1h0c


Resolution: 1.7→40.223 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 3791 4.91 %
Rwork0.1636 73391 -
obs0.1657 77182 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.12 Å2 / Biso mean: 22.5215 Å2 / Biso min: 8.4 Å2
Refinement stepCycle: final / Resolution: 1.7→40.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5947 0 50 802 6799
Biso mean--19.77 32.1 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126250
X-RAY DIFFRACTIONf_angle_d1.1568507
X-RAY DIFFRACTIONf_chiral_restr0.058945
X-RAY DIFFRACTIONf_plane_restr0.0081098
X-RAY DIFFRACTIONf_dihedral_angle_d13.7983801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72150.34391530.27592469262290
1.7215-1.74420.3181340.26212553268790
1.7442-1.76810.28291360.27372597273392
1.7681-1.79330.3411260.25532620274693
1.7933-1.82010.34781360.26122628276492
1.8201-1.84850.28041190.24122643276294
1.8485-1.87880.28961310.23462653278493
1.8788-1.91120.27881670.22932669283695
1.9112-1.9460.26291340.21242670280494
1.946-1.98340.25231260.20142704283096
1.9834-2.02390.25211470.20042674282194
2.0239-2.06790.26221520.19412605275793
2.0679-2.1160.2441440.19212744288896
2.116-2.16890.22071620.18882744290697
2.1689-2.22760.21011310.16892781291297
2.2276-2.29310.23481120.16532815292798
2.2931-2.36710.21261870.15952754294198
2.3671-2.45170.2311250.1542793291898
2.4517-2.54990.17841420.15172764290697
2.5499-2.66590.20611540.1572769292397
2.6659-2.80640.20161310.15222779291096
2.8064-2.98220.20981190.15472766288595
2.9822-3.21230.18551410.15022828296998
3.2123-3.53540.16151570.14262810296797
3.5354-4.04660.19111260.1272824295096
4.0466-5.09670.13231520.12212798295095
5.0967-40.23410.16031470.14692937308495

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