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- PDB-5zbm: Structure of glycolate oxidase containing FMN from Nicotiana bent... -

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Basic information

Entry
Database: PDB / ID: 5zbm
TitleStructure of glycolate oxidase containing FMN from Nicotiana benthamiana
ComponentsGlycolate oxidase
KeywordsOXIDOREDUCTASE / enzyme kinetics / SAXS / oligomerization
Function / homology
Function and homology information


(S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / response to other organism / peroxisome / FMN binding
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 / (S)-2-hydroxy-acid oxidase
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, Z. / Liu, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2018
Title: Structures of glycolate oxidase from Nicotiana benthamiana reveal a conserved pH sensor affecting the binding of FMN.
Authors: Liu, Y. / Wu, W. / Chen, Z.
History
DepositionFeb 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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: Glycolate oxidase
B: Glycolate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1994
Polymers81,2862
Non-polymers9132
Water5,134285
1
A: Glycolate oxidase
hetero molecules

A: Glycolate oxidase
hetero molecules

A: Glycolate oxidase
hetero molecules

A: Glycolate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,3978
Polymers162,5724
Non-polymers1,8254
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 area14960 Å2
ΔGint-81 kcal/mol
Surface area44520 Å2
MethodPISA
2
B: Glycolate oxidase
hetero molecules

B: Glycolate oxidase
hetero molecules

B: Glycolate oxidase
hetero molecules

B: Glycolate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,3978
Polymers162,5724
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area15000 Å2
ΔGint-76 kcal/mol
Surface area45430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.230, 144.230, 129.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Glycolate oxidase


Mass: 40642.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana benthamiana (plant) / Gene: GOX / Production host: Escherichia coli (E. coli) / References: UniProt: E1AXT8
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 4.15 Å3/Da / Density % sol: 70.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35%(w/v) MPD, 0.2M ammonium acetate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.534
11K, H, -L20.466
ReflectionResolution: 2.8→50 Å / Num. obs: 32743 / % possible obs: 90 % / Observed criterion σ(F): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.77 / Num. unique obs: 1473 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GOX

1gox


Resolution: 2.8→45.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.723 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18815 1496 5.1 %RANDOM
Rwork0.17072 ---
obs0.17162 27661 89.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.203 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å2-0 Å2-0 Å2
2---2.23 Å2-0 Å2
3---4.47 Å2
Refinement stepCycle: 1 / Resolution: 2.8→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5388 0 62 287 5737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195548
X-RAY DIFFRACTIONr_bond_other_d0.0020.025430
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9777519
X-RAY DIFFRACTIONr_angle_other_deg0.921312430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51722.941221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32315940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4141547
X-RAY DIFFRACTIONr_chiral_restr0.0650.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216177
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021242
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3454.3472812
X-RAY DIFFRACTIONr_mcbond_other1.3444.3472811
X-RAY DIFFRACTIONr_mcangle_it2.2636.5143508
X-RAY DIFFRACTIONr_mcangle_other2.2636.5143509
X-RAY DIFFRACTIONr_scbond_it1.2574.4342736
X-RAY DIFFRACTIONr_scbond_other1.2574.4352735
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1286.6034012
X-RAY DIFFRACTIONr_long_range_B_refined4.43835.0626637
X-RAY DIFFRACTIONr_long_range_B_other4.39235.0736620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 103 -
Rwork0.213 2015 -
obs--87.09 %

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