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- PDB-2rdw: Crystal Structure of Human Glycolate Oxidase in Complex with Sulfate -

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Basic information

Entry
Database: PDB / ID: 2rdw
TitleCrystal Structure of Human Glycolate Oxidase in Complex with Sulfate
ComponentsHydroxyacid oxidase 1
KeywordsOXIDOREDUCTASE / GOX / HAOX1 / glycolate oxidase / hydroxy acid oxidase / Flavoprotein / FMN / Glycolate pathway / Peroxisome
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
FLAVIN MONONUCLEOTIDE / 2-Hydroxyacid oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMurray, M.S. / Holmes, R.P. / Lowther, W.T.
CitationJournal: Biochemistry / Year: 2008
Title: Active Site and Loop 4 Movements within Human Glycolate Oxidase: Implications for Substrate Specificity and Drug Design.
Authors: Murray, M.S. / Holmes, R.P. / Lowther, W.T.
History
DepositionSep 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Hydroxyacid oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1933
Polymers42,6401
Non-polymers5522
Water3,963220
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)172,77012
Polymers170,5604
Non-polymers2,2108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.649, 143.649, 110.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Hydroxyacid oxidase 1 / HAOX1 / Glycolate oxidase / GOX


Mass: 42640.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAO1, GOX1, HAOX1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES,PEG 600, Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→28.17 Å / Num. obs: 38911 / % possible obs: 92.3 % / Observed criterion σ(I): 3 / Redundancy: 4.83 % / Rmerge(I) obs: 0.05 / Χ2: 0.92 / Net I/σ(I): 18.9 / Scaling rejects: 2007
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.95-2.022.620.2254.2958135971.2886.6
2.02-2.13.180.1945.31204337341.2490
2.1-2.23.920.1836.41562039241.394.5
2.2-2.314.740.1518.21925639931.2594.8
2.31-2.465.160.11910.52073239561.0595
2.46-2.655.010.09511.51965438940.7393.3
2.65-2.914.890.07713.71937139210.8292.8
2.91-3.335.160.05419.92037439080.7892.3
3.33-4.25.590.04227.92195338980.7991.4
4.2-28.177.620.02847.73124240860.6591.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.17 Å
Translation2.5 Å28.17 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2Ldata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOX

1gox


Resolution: 1.95→27.77 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.731 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1971 5.1 %RANDOM
Rwork0.197 ---
obs0.199 38909 92.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 36 220 3050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222922
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9883966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86323.492126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90315525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1431526
X-RAY DIFFRACTIONr_chiral_restr0.130.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022180
X-RAY DIFFRACTIONr_nbd_refined0.2050.21434
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.221
X-RAY DIFFRACTIONr_mcbond_it0.7551.51868
X-RAY DIFFRACTIONr_mcangle_it1.08222899
X-RAY DIFFRACTIONr_scbond_it1.96431232
X-RAY DIFFRACTIONr_scangle_it3.0254.51061
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 138 -
Rwork0.252 2484 -
all-2622 -
obs--85.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1705-0.40130.56720.3462-0.27380.69740.0038-0.3364-0.10520.14350.0120.07430.1636-0.0686-0.01580.16390.00370.03050.08480.0205-0.0412-1.527-20.12926.866
21.4690.02310.15460.6879-0.0140.85810.0356-0.1846-0.43970.08110.005-0.08480.21540.0334-0.04060.19720.042-0.02520.09210.07420.111610.933-36.88523.609
35.2512-1.22390.77575.6010.74663.33450.0548-0.6534-0.34440.74330.0425-0.81030.18590.124-0.09730.22790.0648-0.10060.28890.15180.123823.938-32.79835.81
41.65580.06480.10780.82320.09220.3596-0.03730.0763-0.1593-0.03260.0359-0.07890.12860.08930.00140.13630.03120.00860.07450.0207-0.013810.865-26.79213.464
52.8699-1.04961.95662.0488-1.31483.15610.0262-0.1869-0.29450.00740.04550.13840.2494-0.1954-0.07170.1585-0.01270.07160.08120.03650.0669-8.707-27.82621.974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 6021 - 77
2X-RAY DIFFRACTION2AA61 - 17378 - 190
3X-RAY DIFFRACTION3AA174 - 204191 - 221
4X-RAY DIFFRACTION4AA205 - 318222 - 335
5X-RAY DIFFRACTION5AA319 - 362336 - 379

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