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- PDB-6gmc: 1.2 A resolution structure of human hydroxyacid oxidase 1 bound w... -

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Basic information

Entry
Database: PDB / ID: 6gmc
Title1.2 A resolution structure of human hydroxyacid oxidase 1 bound with FMN and 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole
ComponentsHydroxyacid oxidase 1
KeywordsOXIDOREDUCTASE / glycolate / glyoxylate / peroxisome / FMN / primary hyperoxaluria
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: 1.2 Å
AuthorsMacKinnon, S. / Bezerra, G.A. / Krojer, T. / Smee, C. / Arrowsmith, C.H. / Edwards, E. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106169/ZZ14/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate
Authors: MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Smee, C. / Arrowsmith, C.H. / Edwards, E. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W.
History
DepositionMay 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 27, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.label_alt_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_label_alt_id
Revision 2.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)41,7107
Polymers40,7341
Non-polymers9766
Water5,459303
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)166,84128
Polymers162,9364
Non-polymers3,90524
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 area18560 Å2
ΔGint-2 kcal/mol
Surface area45950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.348, 97.348, 80.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 40733.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAO1, GOX1, HAOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#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: Chemical ChemComp-C7C / 5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylate


Mass: 271.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H4ClN2O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 -- 10% ethylene glycol -- 0.1M bis-tris-propane pH 7.5 -- 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.2→68.835 Å / Num. all: 115996 / Num. obs: 115996 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.088 / Rsym value: 0.076 / Net I/av σ(I): 4.3 / Net I/σ(I): 8.9 / Num. measured all: 484713
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.264.10.6881.168466169050.3860.7930.6881.899.5
1.26-1.344.10.4741.665349159840.2640.5450.4742.799.5
1.34-1.434.10.3262.362585150870.1810.3750.3263.999.7
1.43-1.554.20.2033.658365139790.1130.2330.2035.999.6
1.55-1.74.20.1375.254069129250.0760.1580.1378.499.6
1.7-1.94.30.096749835116850.0540.1110.09611.699.6
1.9-2.194.30.0699.243801102710.0380.0790.0691699.5
2.19-2.684.30.0599.93763587310.0330.0680.05919.499.5
2.68-3.794.30.0569.62870267050.0310.0640.05622.298.7
3.79-38.2794.30.069.71590637240.0330.0690.0623.798.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NZL

2nzl


Resolution: 1.2→38.31 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.144 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1548 5723 4.9 %RANDOM
Rwork0.1342 ---
obs0.1352 110271 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.97 Å2 / Biso mean: 16.823 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å20 Å2
2---0.22 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.2→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 63 303 3130
Biso mean--14.83 30.07 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0143047
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172815
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.6744155
X-RAY DIFFRACTIONr_angle_other_deg1.0151.6526594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86621.351148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81215533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7361524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
X-RAY DIFFRACTIONr_rigid_bond_restr0.97535862
X-RAY DIFFRACTIONr_sphericity_free21.4695198
X-RAY DIFFRACTIONr_sphericity_bonded11.21755894
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 397 -
Rwork0.258 8145 -
all-8542 -
obs--99.37 %

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