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- PDB-2w0u: CRYSTAL STRUCTURE OF HUMAN GLYCOLATE OXIDASE IN COMPLEX WITH THE ... -

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Basic information

Entry
Database: PDB / ID: 2w0u
TitleCRYSTAL STRUCTURE OF HUMAN GLYCOLATE OXIDASE IN COMPLEX WITH THE INHIBITOR 5-[(4-CHLOROPHENYL)SULFANYL]- 1,2,3-THIADIAZOLE-4-CARBOXYLATE.
ComponentsHYDROXYACID OXIDASE 1
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / GLYCOLATE PATHWAY / HYDROXYACID OXIDASE 1 / PEROXISOME / INHIBITOR
Function / homology
Function and homology information


glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / fatty acid alpha-oxidation / (S)-2-hydroxy-acid oxidase activity / Glyoxylate metabolism and glycine degradation / glycine biosynthetic process / peroxisomal matrix / Peroxisomal protein import ...glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / fatty acid alpha-oxidation / (S)-2-hydroxy-acid oxidase activity / Glyoxylate metabolism and glycine degradation / glycine biosynthetic process / peroxisomal matrix / Peroxisomal protein import / peroxisome / FMN binding / response to oxidative stress / intracellular membrane-bounded organelle / cytosol
Similarity search - Function
Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-C7C / FLAVIN MONONUCLEOTIDE / 2-Hydroxyacid oxidase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsBourhis, J.M. / Lindqvist, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of Human Glycolate Oxidase in Complex with the Inhibitor 4-Carboxy-5-[(4-Chlorophenyl)Sulfanyl]-1,2,3-Thiadiazole.
Authors: Bourhis, J.M. / Vignaud, C. / Pietrancosta, N. / Gueritte, F. / Guenard, D. / Lederer, F. / Lindqvist, Y.
History
DepositionOct 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYDROXYACID OXIDASE 1
B: HYDROXYACID OXIDASE 1
C: HYDROXYACID OXIDASE 1
D: HYDROXYACID OXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,81712
Polymers163,9054
Non-polymers2,9128
Water59433
1
A: HYDROXYACID OXIDASE 1
hetero molecules

A: HYDROXYACID OXIDASE 1
hetero molecules

A: HYDROXYACID OXIDASE 1
hetero molecules

A: HYDROXYACID OXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,81712
Polymers163,9054
Non-polymers2,9128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area13840 Å2
ΔGint-66.1 kcal/mol
Surface area45320 Å2
MethodPISA
2
B: HYDROXYACID OXIDASE 1
hetero molecules

B: HYDROXYACID OXIDASE 1
hetero molecules

B: HYDROXYACID OXIDASE 1
hetero molecules

B: HYDROXYACID OXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,81712
Polymers163,9054
Non-polymers2,9128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area14050 Å2
ΔGint-63.29 kcal/mol
Surface area44820 Å2
MethodPISA
3
C: HYDROXYACID OXIDASE 1
hetero molecules

C: HYDROXYACID OXIDASE 1
hetero molecules

C: HYDROXYACID OXIDASE 1
hetero molecules

C: HYDROXYACID OXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,81712
Polymers163,9054
Non-polymers2,9128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area14080 Å2
ΔGint-69.76 kcal/mol
Surface area44550 Å2
MethodPISA
4
D: HYDROXYACID OXIDASE 1
hetero molecules

D: HYDROXYACID OXIDASE 1
hetero molecules

D: HYDROXYACID OXIDASE 1
hetero molecules

D: HYDROXYACID OXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,81712
Polymers163,9054
Non-polymers2,9128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area14100 Å2
ΔGint-58.38 kcal/mol
Surface area45170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.690, 138.690, 186.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
HYDROXYACID OXIDASE 1 / GLYCOLATE OXIDASE / HAOX1 / GOX


Mass: 40976.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Plasmid: PTRCHISB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase
#2: Chemical
ChemComp-C7C / 5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylate


Mass: 271.723 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H4ClN2O2S2
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.07 Å3/Da / Density % sol: 59.62 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALLISATION WAS PERFORMED BY THE HANGING DROP VAPOR DIFFUSION METHOD, USING A PRECIPITANT SOLUTION CONTAINING 200 MM NACL, 100 MM MMT AT PH 7.5, AND 15% (W/V) POLYETHYLENE GLYCOL 1000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.8→47.4 Å / Num. obs: 43574 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NZL

2nzl


Resolution: 2.84→46.73 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.883 / SU B: 13.918 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2179 5 %RANDOM
Rwork0.205 ---
obs0.207 41393 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.84→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10344 0 188 33 10565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210709
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.99114498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63951325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12623.484442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.131151900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281590
X-RAY DIFFRACTIONr_chiral_restr0.0780.21652
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027866
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.24757
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.27297
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.2190
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6521.56801
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.844210579
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.10934640
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7444.53919
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.91 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 152
Rwork0.284 2888

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