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- PDB-7ns7: Human L-alanine:glyoxylate aminotransferase minor allele variant:... -

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Basic information

Entry
Database: PDB / ID: 7ns7
TitleHuman L-alanine:glyoxylate aminotransferase minor allele variant: AGXT-Mi (P11L-I340M)
ComponentsL-alanine:glyoxylate aminotransferase
KeywordsTRANSFERASE / alanine-glyoxylate transaminase / alanine-glyoxylate aminotransferase / alanine-glyoxylic aminotransferase / L-alanine-glycine transaminase / pyrodoxal / disorder
Function / homology
Function and homology information


oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process ...oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process / glyoxylate catabolic process / Glyoxylate metabolism and glycine degradation / transaminase activity / amino acid binding / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / peroxisome / : / pyridoxal phosphate binding / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsCellini, B. / Dindo, M.
CitationJournal: Protein Sci. / Year: 2022
Title: Structural dynamics shape the fitness window of alanine:glyoxylate aminotransferase.
Authors: Dindo, M. / Pascarelli, S. / Chiasserini, D. / Grottelli, S. / Costantini, C. / Uechi, G.I. / Giardina, G. / Laurino, P. / Cellini, B.
History
DepositionMar 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-alanine:glyoxylate aminotransferase
B: L-alanine:glyoxylate aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,6502
Polymers86,6502
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The model is equivalent to the biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-45 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.590, 90.590, 140.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein L-alanine:glyoxylate aminotransferase / Alanine-glyoxylate aminotransferase / Serine-pyruvate aminotransferase


Mass: 43325.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: polymorphic variant P11L-I340M. PLP bound to K209 internal aldimine form
Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT / Variant: P11L / Production host: Escherichia coli (E. coli)
References: UniProt: P21549, alanine-glyoxylate transaminase, serine-pyruvate transaminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.12 % / Description: diamond shaped yellow crystals
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 mixing of: Protein: 0.04M AGT-Mi solution in 0.1M KPhO Precipitant: 0.03M MgCl2 , 0.03M CaCl2 , 0.05M HEPES 0.05M MOPS at a final pH 7.5, 40% v/v Ethylene glycol; 20% w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 8, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.505
11-K, -H, -L20.495
ReflectionResolution: 2.2→64.06 Å / Num. obs: 57290 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.061 / Rrim(I) all: 0.125 / Net I/σ(I): 9.3 / Num. measured all: 214921 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.263.80.3691684244370.7880.2130.4293.699.5
9.59-64.063.90.05428137160.9950.0290.06220.698.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F9S

5f9s


Resolution: 2.2→64.06 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.831 / SU B: 5.292 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2894 5660 9.9 %RANDOM
Rwork0.2407 ---
obs0.2455 51579 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.54 Å2 / Biso mean: 26.561 Å2 / Biso min: 5.95 Å2
Baniso -1Baniso -2Baniso -3
1-11.61 Å20 Å20 Å2
2--11.61 Å20 Å2
3----23.23 Å2
Refinement stepCycle: final / Resolution: 2.2→64.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5202 0 0 75 5277
Biso mean---17.93 -
Num. residues----681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135318
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174993
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6327229
X-RAY DIFFRACTIONr_angle_other_deg1.4121.56711551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1621.917240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.4215848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3761532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025921
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021075
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 373 -
Rwork0.291 3831 -
all-4204 -
obs--99.24 %

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