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- PDB-5f9s: Crystal structure of human Alanine:Glyoxylate Aminotransferase ma... -

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Basic information

Entry
Database: PDB / ID: 5f9s
TitleCrystal structure of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.7 Angstrom; 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
PYRIDOXAL-5'-PHOSPHATE / 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 States, 2items
OrganizationGrant numberCountry
Oxalosis and Hyperoxaluria FoundationOHF2011 United States
European Community's Seventh Framework Programme (FP7/2007-2013)BioStruct-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
DepositionDec 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: 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 / diffrn_radiation_wavelength / 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

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Assembly

Deposited unit
A: Serine--pyruvate aminotransferase
B: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2804
Polymers84,7862
Non-polymers4942
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-55 kcal/mol
Surface area26230 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 / Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) / 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#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: 2.14 Å3/Da / Density % sol: 42.47 % / 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: 5-6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 150 frames, osc. 0.75 degrees
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: 70070 / % possible obs: 87 % / Redundancy: 4.2 % / Biso Wilson estimate: 20.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.042 / Net I/σ(I): 10.6 / Num. measured all: 294083 / Scaling rejects: 113
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
1.7-1.733.90.6141.61373935100.7550.32483.4
9-48.044.80.03130.524965190.9970.01582.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.552
Highest resolutionLowest resolution
Rotation45.12 Å1.91 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
Aimless0.3.11data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
Coot0.8.2model building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hoc

1hoc


Resolution: 1.7→45.118 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 3411 4.87 %
Rwork0.1583 66599 -
obs0.1605 70010 86.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.01 Å2 / Biso mean: 22.7206 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 1.7→45.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5977 0 0 802 6779
Biso mean---32.02 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116252
X-RAY DIFFRACTIONf_angle_d1.158511
X-RAY DIFFRACTIONf_chiral_restr0.056945
X-RAY DIFFRACTIONf_plane_restr0.0071098
X-RAY DIFFRACTIONf_dihedral_angle_d14.6173803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72430.29961570.23442574273183
1.7243-1.750.27711390.2252663280283
1.75-1.77740.29781300.23932700283085
1.7774-1.80650.3241240.22362720284485
1.8065-1.83770.27521460.22642683282985
1.8377-1.87110.26191310.21412747287886
1.8711-1.90710.26241530.21212710286387
1.9071-1.9460.25751430.2092773291686
1.946-1.98830.26981370.19812791292887
1.9883-2.03460.26251520.1932754290687
2.0346-2.08540.24661540.18782776293087
2.0854-2.14180.24841500.18542783293387
2.1418-2.20490.22481440.17422806295088
2.2049-2.2760.23671160.16052869298588
2.276-2.35740.21931740.15872820299489
2.3574-2.45170.22711280.15232842297088
2.4517-2.56330.19371470.14982832297988
2.5633-2.69840.18821570.1532788294587
2.6984-2.86750.19811380.14712836297487
2.8675-3.08880.20111250.14852788291386
3.0888-3.39960.17841480.14322824297286
3.3996-3.89130.17041320.12992826295886
3.8913-4.90170.14571350.11942805294085
4.9017-45.13390.16041510.14462889304083

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