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- PDB-5qid: PanDDA analysis group deposition of models with modelled events (... -

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Basic information

Entry
Database: PDB / ID: 5qid
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z1787627869
ComponentsHydroxyacid oxidase 1
KeywordsOXIDOREDUCTASE / PanDDA / SGC - Diamond I04-1 fragment screening / HAO1 / XChemExplorer
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 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 / Chem-GWY / 2-Hydroxyacid oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.45 Å
AuthorsMacKinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Authors: MacKinnon, S. / Bezerra, G.A. / Krojer, T. / Bradley, A.R. / Talon, R. / Brandao-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. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Brennan, P.E. / Yue, W.W.
History
DepositionMay 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)41,5053
Polymers40,8211
Non-polymers6842
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.487, 97.487, 80.388
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: 40820.992 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GWY / 5-chloranyl-~{N}-methyl-~{N}-[[(3~{S})-oxolan-3-yl]methyl]pyrimidin-4-amine


Mass: 227.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14ClN3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.34 Å3/Da / Density % sol: 47.42 % / Mosaicity: 0.06 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.75 / Details: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.45→26.16 Å / Num. obs: 66577 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 17.4 / Num. measured all: 392437 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.493.80.5671821948300.7820.3360.6622.198.7
6.48-26.166.50.03550527730.9990.0150.03850.598.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2NZL

2nzl


Resolution: 1.45→68.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.37 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 3400 5.1 %RANDOM
Rwork0.1797 ---
obs0.1806 63175 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.74 Å2 / Biso mean: 19.904 Å2 / Biso min: 7.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å20 Å2
2---0.6 Å20 Å2
3---1.2 Å2
Refinement stepCycle: final / Resolution: 1.45→68.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 61 139 2808
Biso mean--18.01 21.47 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024525
X-RAY DIFFRACTIONr_bond_other_d0.0020.023494
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.9815180
X-RAY DIFFRACTIONr_angle_other_deg1.00938063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27322.961152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09115604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8411535
X-RAY DIFFRACTIONr_chiral_restr0.1090.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214525
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02812
X-RAY DIFFRACTIONr_mcbond_it1.3691.9512332
X-RAY DIFFRACTIONr_mcbond_other1.3691.9512332
X-RAY DIFFRACTIONr_mcangle_it2.1022.8062487
LS refinement shellResolution: 1.449→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 254 -
Rwork0.259 4583 -
all-4837 -
obs--98.94 %

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