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- PDB-7r4o: Structure of human hydroxyacid oxidase 1 bound with 2-((4H-1,2,4-... -

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Basic information

Entry
Database: PDB / ID: 7r4o
TitleStructure of human hydroxyacid oxidase 1 bound with 2-((4H-1,2,4-triazol-3-yl)thio)-1-(4-(3-chlorophenyl)piperazin-1-yl)ethan-1-one
ComponentsHydroxyacid oxidase 1
KeywordsOXIDOREDUCTASE / HAO1 / hydroxyacid oxidase / glycolate oxidase / fragment screening
Function / homology
Function and homology information


glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / fatty acid alpha-oxidation / glycine biosynthetic process / Glyoxylate metabolism and glycine degradation / peroxisomal matrix / Peroxisomal protein import ...glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / fatty acid alpha-oxidation / glycine biosynthetic process / Glyoxylate metabolism and glycine degradation / peroxisomal matrix / Peroxisomal protein import / 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-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-I2W / 2-Hydroxyacid oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMackinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandeo-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Mackinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandeo-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of human hydroxyacid oxidase 1 bound with 5-bromo-N-methyl-1H-indazole-3-carboxamide
Authors: Mackinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandeo-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / ...Authors: Mackinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandeo-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W.
History
DepositionFeb 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)40,9463
Polymers40,1521
Non-polymers7942
Water5,098283
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)163,78612
Polymers160,6094
Non-polymers3,1778
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 area14070 Å2
ΔGint-62 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.060, 97.060, 80.220
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: 40152.258 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 BL21(DE3) (bacteria) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase
#2: Chemical ChemComp-I2W / 2-((4H-1,2,4-triazol-3-yl)thio)-1-(4-(3-chlorophenyl)piperazin-1-yl)ethan-1-one


Mass: 337.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16ClN5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MIB, pH 7; 30% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.29→61.91 Å / Num. obs: 88617 / % possible obs: 95 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.29-1.321.50.576689545520.5710.5310.786166.2
5.77-61.836.30.032687210860.9980.0140.03546.399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GMB

6gmb


Resolution: 1.5→61.91 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.064 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 3040 5.1 %RANDOM
Rwork0.1632 ---
obs0.1644 56358 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.42 Å2 / Biso mean: 16.839 Å2 / Biso min: 8.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.27 Å2
Refinement stepCycle: final / Resolution: 1.5→61.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 53 283 2914
Biso mean--26.43 28.65 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132890
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152758
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.6463962
X-RAY DIFFRACTIONr_angle_other_deg1.5551.5866330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.03120.638141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26615478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6071526
X-RAY DIFFRACTIONr_chiral_restr0.0970.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023435
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02671
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 250 -
Rwork0.194 4117 -
all-4367 -
obs--99.77 %

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