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

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Basic information

Entry
Database: PDB / ID: 5luc
TitleCrystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site
ComponentsSerine--pyruvate aminotransferase
KeywordsTRANSFERASE / Primary Hyperoxaluria Type I / PH1
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: 1.8 Å
AuthorsGiardina, G. / Cutruzzola, F. / Cellini, B. / Borri Voltattorni, C. / 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
DepositionSep 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
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 17, 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
E: Serine--pyruvate aminotransferase
G: Serine--pyruvate aminotransferase
M: Serine--pyruvate aminotransferase
N: Serine--pyruvate aminotransferase
S: Serine--pyruvate aminotransferase
T: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,89224
Polymers354,2418
Non-polymers3,65116
Water74,8344154
1
A: Serine--pyruvate aminotransferase
B: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4736
Polymers88,5602
Non-polymers9134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-48 kcal/mol
Surface area26300 Å2
MethodPISA
2
E: Serine--pyruvate aminotransferase
G: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4736
Polymers88,5602
Non-polymers9134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-46 kcal/mol
Surface area26150 Å2
MethodPISA
3
M: Serine--pyruvate aminotransferase
N: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4736
Polymers88,5602
Non-polymers9134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint-44 kcal/mol
Surface area26260 Å2
MethodPISA
4
S: Serine--pyruvate aminotransferase
T: Serine--pyruvate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4736
Polymers88,5602
Non-polymers9134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-48 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.599, 141.107, 256.117
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: 44280.152 Da / Num. of mol.: 8 / Mutation: D183N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Organ: liver / Variant: D183N / Plasmid: PTRCHIS2A / 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.: 8 / Mutation: D183N
Source method: isolated from a genetically manipulated source
Formula: C8H10NO6P / References: serine-pyruvate transaminase
#3: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4154 / 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: 3.37 Å3/Da / Density % sol: 63.5 % / Description: Dimond shapes yellow xtals after 1 week
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: mixing equal volumes of protein solution: 15 mg/ml in 40 mM PhO pH 7.4 - 60 mM Hepes pH 7.0 reservoir: ammonium acetate o.1 M - BIS TRIS pH 5.5 0.1M - 17% PEG 10K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.8→57.23 Å / Num. obs: 397712 / % possible obs: 94.2 % / Redundancy: 4.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.151 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.834.10.7220.707196.1
9.86-57.234.70.0960.986183.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation48.05 Å1.89 Å

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f9s

5f9s


Resolution: 1.8→56.692 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.64
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 19829 4.99 %random selection
Rwork0.1631 ---
obs0.1646 397475 93.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.49 Å2 / Biso mean: 14.9516 Å2 / Biso min: 3.87 Å2
Refinement stepCycle: final / Resolution: 1.8→56.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23741 0 112 4154 28007
Biso mean--19.85 24.5 -
Num. residues----3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02224716
X-RAY DIFFRACTIONf_angle_d1.59833643
X-RAY DIFFRACTIONf_chiral_restr0.0993748
X-RAY DIFFRACTIONf_plane_restr0.0114328
X-RAY DIFFRACTIONf_dihedral_angle_d16.39914793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.29576910.2404127461343795
1.8205-1.84190.28596600.2297128531351397
1.8419-1.86430.28266630.2218129261358997
1.8643-1.88790.25336890.2099128341352396
1.8879-1.91280.24576190.2079129061352596
1.9128-1.9390.25696740.2052128621353696
1.939-1.96670.24656640.201128751353996
1.9667-1.9960.24316420.1959129021354496
1.996-2.02720.22316380.1922128971353596
2.0272-2.06050.22976990.1869128111351096
2.0605-2.0960.19996390.1799128131345296
2.096-2.13410.19796620.1738127071336995
2.1341-2.17520.20216720.1683124581313093
2.1752-2.21960.21066780.1713127251340395
2.2196-2.26780.20186390.1654127721341195
2.2678-2.32060.18936440.1655127701341495
2.3206-2.37860.27070.166126131332095
2.3786-2.44290.20686740.1681126471332194
2.4429-2.51480.1986680.1686125561322494
2.5148-2.5960.21346820.1677125471322994
2.596-2.68880.1836580.156125301318893
2.6888-2.79640.19196980.1578124811317993
2.7964-2.92370.20286350.1553124601309592
2.9237-3.07780.1836410.1554123891303092
3.0778-3.27060.17966470.1531121731282090
3.2706-3.52310.16556410.1442123761301791
3.5231-3.87760.16026750.1383121941286990
3.8776-4.43850.14766710.1283120891276089
4.4385-5.59130.13956070.1333120431265088
5.5913-56.71970.15846520.1545116911234383

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