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- PDB-1j04: Structural mechanism of enzyme mistargeting in hereditary kidney ... -

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Basic information

Entry
Database: PDB / ID: 1j04
TitleStructural mechanism of enzyme mistargeting in hereditary kidney stone disease in vitro
Componentsalanine--glyoxylate aminotransferase
KeywordsTRANSFERASE / Aminotransferase / Pyridoxal phosphate
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 / glyoxylate catabolic process / L-serine metabolic 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 / glyoxylate catabolic process / L-serine metabolic process / L-cysteine catabolic process / Glyoxylate metabolism and glycine degradation / amino acid binding / transaminase activity / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / peroxisome / protein self-association / 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
(AMINOOXY)ACETIC ACID / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, X. / Djordjevic, S. / Bartlam, M. / Ye, S. / Rao, Z. / Danpure, C.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structural implications of a G170R mutation of alanine:glyoxylate aminotransferase that is associated with peroxisome-to-mitochondrion mistargeting.
Authors: Djordjevic, S. / Zhang, X. / Bartlam, M. / Ye, S. / Rao, Z. / Danpure, C.J.
History
DepositionOct 30, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 25, 2018Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / software / struct_ref_seq_dif
Item: _entity.src_method / _software.version
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alanine--glyoxylate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1279
Polymers43,3911
Non-polymers7368
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: alanine--glyoxylate aminotransferase
hetero molecules

A: alanine--glyoxylate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,25418
Polymers86,7822
Non-polymers1,47116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-11
Buried area11160 Å2
ΔGint-53 kcal/mol
Surface area27280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.491, 89.491, 142.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 43391.098 Da / Num. of mol.: 1 / Mutation: G170R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase
#2: Chemical ChemComp-AOA / (AMINOOXY)ACETIC ACID / Aminooxyacetic acid


Mass: 91.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.24 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2002
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 231743 / Num. obs: 18539 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.6
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1497 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0C
Resolution: 2.6→47.4 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1763 -RANDOM
Rwork0.223 ---
all-18489 --
obs-17989 97.2 %-
Displacement parametersBiso mean: 41.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.909 Å20 Å2-2.909 Å2
2--0 Å20 Å2
3---5.817 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 48 113 3148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.293 201 -
Rwork0.296 --
obs-2092 92.6 %

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