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- PDB-2yob: High resolution AGXT_M structure -

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Basic information

Entry
Database: PDB / ID: 2yob
TitleHigh resolution AGXT_M structure
ComponentsSERINE--PYRUVATE AMINOTRANSFERASE
KeywordsTRANSFERASE / PRIMARY HYPEROXALURIA TYPE I / AGXT FOLDING AND STABILITY DEFECTS
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
PYRIDOXAL-5'-PHOSPHATE / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFabelo-Rosa, I. / Mesa-Torres, N. / Riverol, D. / Yunta, C. / Albert, A. / Salido, E. / Pey, A.L.
CitationJournal: Plos One / Year: 2013
Title: The Role of Protein Denaturation Energetics and Molecular Chaperones in the Aggregation and Mistargeting of Mutants Causing Primary Hyperoxaluria Type I
Authors: Mesa-Torres, N. / Fabelo-Rosa, I. / Riverol, D. / Yunta, C. / Albert, A. / Salido, E. / Pey, A.L.
History
DepositionOct 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)86,62414
Polymers84,9662
Non-polymers1,65712
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-68.4 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.495, 103.525, 153.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SERINE--PYRUVATE AMINOTRANSFERASE / SPT / ALANINE--GLYOXYLATE AMINOTRANSFERASE / AGT


Mass: 42483.066 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCOLDII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21549

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Non-polymers , 5 types, 714 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): SCHIFF BASE WITH K209

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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: 2.52 Å3/Da / Density % sol: 51.28 % / Description: NONE
Crystal growDetails: 15% PEG 3350, 0.1M BIS-TRIS PH 5.2, 150MM LI2SO4 AND 5% W/V OCTYL-B-D-GLUCOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.9→48.22 Å / Num. obs: 69440 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 25.79 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.91→2 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0C

1h0c


Resolution: 1.9→45.95 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 3507 5.1 %
Rwork0.1695 --
obs0.1713 69358 99.82 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.749 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.9646 Å20 Å20 Å2
2---4.8576 Å20 Å2
3----0.107 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5928 0 104 702 6734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076160
X-RAY DIFFRACTIONf_angle_d1.0648348
X-RAY DIFFRACTIONf_dihedral_angle_d17.2362316
X-RAY DIFFRACTIONf_chiral_restr0.072924
X-RAY DIFFRACTIONf_plane_restr0.0051062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8998-1.92590.33991190.3182522X-RAY DIFFRACTION96
1.9259-1.95340.30021250.29992654X-RAY DIFFRACTION100
1.9534-1.98250.33941400.25142546X-RAY DIFFRACTION100
1.9825-2.01350.25861440.22212628X-RAY DIFFRACTION100
2.0135-2.04650.25631280.20252587X-RAY DIFFRACTION100
2.0465-2.08180.2561280.18122627X-RAY DIFFRACTION100
2.0818-2.11970.20441380.16752615X-RAY DIFFRACTION100
2.1197-2.16040.22611370.16892602X-RAY DIFFRACTION100
2.1604-2.20450.23251390.18222624X-RAY DIFFRACTION100
2.2045-2.25250.28061420.22912602X-RAY DIFFRACTION100
2.2525-2.30490.30251250.20882607X-RAY DIFFRACTION100
2.3049-2.36250.21171590.16912615X-RAY DIFFRACTION100
2.3625-2.42640.20941330.16352612X-RAY DIFFRACTION100
2.4264-2.49780.22591280.16362648X-RAY DIFFRACTION100
2.4978-2.57840.2091470.16292627X-RAY DIFFRACTION100
2.5784-2.67050.20011280.15772610X-RAY DIFFRACTION100
2.6705-2.77750.22881390.16492651X-RAY DIFFRACTION100
2.7775-2.90380.18881440.16862635X-RAY DIFFRACTION100
2.9038-3.05690.23021630.16852626X-RAY DIFFRACTION100
3.0569-3.24840.19741460.16642663X-RAY DIFFRACTION100
3.2484-3.49910.22011310.16352658X-RAY DIFFRACTION100
3.4991-3.85110.17191670.15772649X-RAY DIFFRACTION100
3.8511-4.4080.15281580.13682679X-RAY DIFFRACTION100
4.408-5.55210.15881360.13562731X-RAY DIFFRACTION100
5.5521-45.96310.17521630.16322833X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -9.5159 Å / Origin y: 14.9471 Å / Origin z: -38.9801 Å
111213212223313233
T0.0151 Å20.0053 Å2-0.0465 Å2-0.0671 Å2-0.0036 Å2--0.0946 Å2
L0.3308 °2-0.001 °2-0.1869 °2-1.306 °2-0.0183 °2--1.1941 °2
S0.0152 Å °0.0059 Å °-0.0024 Å °-0.1744 Å °0.0235 Å °0.2083 Å °-0.0025 Å °-0.0365 Å °-0.0115 Å °
Refinement TLS groupSelection details: ALL

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