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- PDB-6gmb: Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate -

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Basic information

Entry
Database: PDB / ID: 6gmb
TitleStructure of human hydroxyacid oxidase 1 bound with FMN and glycolate
ComponentsHydroxyacid oxidase 1
KeywordsOXIDOREDUCTASE / glycolate / glyoxylate / peroxisome / FMN / primary hyperoxaluria / Structural Genomics / Structural Genomics Consortium / SGC
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 / GLYCOLIC ACID / 2-Hydroxyacid oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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. / Structural Genomics Consortium (SGC)
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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxyacid oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1278
Polymers40,1521
Non-polymers9757
Water6,774376
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)164,50932
Polymers160,6094
Non-polymers3,90028
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 area19960 Å2
ΔGint9 kcal/mol
Surface area45940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.431, 97.431, 80.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-945-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 (E. coli) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase

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Non-polymers , 5 types, 383 molecules

#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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 30% PEG1000 -- 0.1M MIB pH 8.0

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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: 1.35→68.894 Å / Num. all: 81521 / Num. obs: 81521 / % possible obs: 99.2 % / Redundancy: 6.2 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Rsym value: 0.04 / Net I/av σ(I): 8 / Net I/σ(I): 29.2 / Num. measured all: 502198
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
1.35-1.423.90.0937.244710113290.0520.1070.0931194.9
1.42-1.515.80.0778.465858112890.0350.0850.07717.4100
1.51-1.616.70.0641071509106710.0270.0690.06423.2100
1.61-1.746.70.05411.56634299110.0230.0590.05427.5100
1.74-1.916.70.04612.86083891290.0190.050.04632.4100
1.91-2.136.60.04113.85448782590.0170.0440.04137.8100
2.13-2.466.70.03814.74848572850.0160.0410.03841.999.9
2.46-3.026.60.03715.44114661950.0150.040.03744.299.9
3.02-4.276.60.03614.93142147850.0150.0390.03646.699.9
4.27-40.1826.50.039141740226680.0160.0420.0394799.8

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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: 1.35→40.21 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.842 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1302 3976 4.9 %RANDOM
Rwork0.11 ---
obs0.111 77545 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.99 Å2 / Biso mean: 14.354 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 1.35→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 56 376 3223
Biso mean--17.46 29.19 -
Num. residues----362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0142996
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172801
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.6694079
X-RAY DIFFRACTIONr_angle_other_deg0.9871.6526563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.51521.486148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0541524
X-RAY DIFFRACTIONr_chiral_restr0.0630.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
X-RAY DIFFRACTIONr_rigid_bond_restr0.74335797
X-RAY DIFFRACTIONr_sphericity_free22.8995231
X-RAY DIFFRACTIONr_sphericity_bonded8.30755878
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.131 289 -
Rwork0.096 5284 -
all-5573 -
obs--92.19 %

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