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- PDB-6rv0: human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma); ... -

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Basic information

Entry
Database: PDB / ID: 6rv0
Titlehuman Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma); with PMP 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 / 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 / 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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsGiardina, G. / Cutruzzola, F. / Cellini, B. / Mirco, D.
CitationJournal: Biochem.J. / Year: 2019
Title: Cycloserine enantiomers are reversible inhibitors of human alanine:glyoxylate aminotransferase: implications for Primary Hyperoxaluria type 1.
Authors: Dindo, M. / Grottelli, S. / Annunziato, G. / Giardina, G. / Pieroni, M. / Pampalone, G. / Faccini, A. / Cutruzzola, F. / Laurino, P. / Costantino, G. / Cellini, B.
History
DepositionMay 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Assembly

Deposited unit
A: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3112
Polymers43,0631
Non-polymers2481
Water23413
1
A: Serine--pyruvate aminotransferase
hetero molecules

A: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6224
Polymers86,1262
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8990 Å2
ΔGint-57 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.306, 90.306, 142.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

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Components

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


Mass: 43062.840 Da / Num. of mol.: 1
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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-12% PEG 6K; 5% 2-methyl-2,4-pentanediol (MPD); 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→47.49 Å / Num. obs: 16712 / % possible obs: 99.5 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.025 / Rrim(I) all: 0.074 / Net I/σ(I): 15.8 / Num. measured all: 141538
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
2.7-2.838.41.121851622020.7340.4021.1931.9100
8.96-47.497.40.02938685240.9990.0110.03149.497

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.413
Highest resolutionLowest resolution
Rotation47.49 Å3.25 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F9S

5f9s


Resolution: 2.7→47.49 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 25.189 / SU ML: 0.444 / SU R Cruickshank DPI: 0.5996 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.6 / ESU R Free: 0.384
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3253 773 4.6 %RANDOM
Rwork0.2595 ---
obs0.2623 15911 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 195.66 Å2 / Biso mean: 90.111 Å2 / Biso min: 40.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2--2.69 Å20 Å2
3----5.38 Å2
Refinement stepCycle: final / Resolution: 2.7→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 16 13 2918
Biso mean--53.35 64.06 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132998
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172738
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.6344093
X-RAY DIFFRACTIONr_angle_other_deg1.211.5666348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8485391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0922.296135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78515464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8451516
X-RAY DIFFRACTIONr_chiral_restr0.060.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02601
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 58 -
Rwork0.45 1170 -
all-1228 -
obs--99.92 %

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