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- PDB-1al8: THREE-DIMENSIONAL STRUCTURE OF GLYCOLATE OXIDASE WITH BOUND ACTIV... -

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Basic information

Entry
Database: PDB / ID: 1al8
TitleTHREE-DIMENSIONAL STRUCTURE OF GLYCOLATE OXIDASE WITH BOUND ACTIVE-SITE INHIBITORS
ComponentsGLYCOLATE OXIDASE
KeywordsFLAVOPROTEIN / DRUG DESIGN / INHIBITOR BINDING
Function / homology
Function and homology information


oxidative photosynthetic carbon pathway / (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
3-DECYL-2,5-DIOXO-4-HYDROXY-3-PYRROLINE / FLAVIN MONONUCLEOTIDE / Glycolate oxidase
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStenberg, K. / Lindqvist, Y.
Citation
Journal: Protein Sci. / Year: 1997
Title: Three-dimensional structures of glycolate oxidase with bound active-site inhibitors.
Authors: Stenberg, K. / Lindqvist, Y.
#1: Journal: Protein Expr.Purif. / Year: 1996
Title: High-Level Expression, Purification and Crystallization of Recombinant Spinach Glycolate Oxidase in Escherichia Coli
Authors: Stenberg, K. / Lindqvist, Y.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Refined Structure of Spinach Glycolate Oxidase at 2 A Resolution
Authors: Lindqvist, Y.
History
DepositionJun 12, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOLATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0463
Polymers39,3361
Non-polymers7102
Water1,22568
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)160,18412
Polymers157,3454
Non-polymers2,8398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area14290 Å2
ΔGint-42 kcal/mol
Surface area50930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.400, 95.400, 93.500
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: 39336.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE STRUCTURE DESCRIBED IS A COMPLEX OF GLYCOLATE OXIDASE WITH FMN AND AN INHIBITOR
Source: (gene. exp.) Spinacia oleracea (spinach) / Cell line: BL21 / Cellular location: PEROXISOME / Plasmid: PKS20+ / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P05414, (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-DHP / 3-DECYL-2,5-DIOXO-4-HYDROXY-3-PYRROLINE


Type: L-peptide linking / Mass: 253.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.5 Å3/Da / Density % sol: 54.5 %
Crystal growpH: 8.3
Details: PROTEIN WAS CRYSTALLIZED FROM 50MM TRIS- BUFFER, 0.25 MG/ML FMN, 4% TERTIARY BUTANOL AND 0.5 % JF 5969, PH 8.3. JF 5969 IS A MIXTURE OF SYMPERONIC NPE1800 (33.3G/L), TWEEN 85 (20G/L) IN CYCLOHEXANONE.
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
20.05 MTris-HCl11
30.5 mg/mlGOX11
40.25 mg/mlFMN11
50.5 %JF596911
65 %(v/v)tertiary butanol12
712

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 21308 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 0.317 Å2 / Rsym value: 0.094 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.369 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 237398 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.369

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOX

1gox


Resolution: 2.2→8 Å / Data cutoff low absF: 0 / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
Details: TOPOLOGY AND PARAMETER FILES FOR THE TKP-INHIBITOR WERE CREATED USING THE PROGRAM XPLO2D (REF: [O/X-PLOR DICTIONARIES] G.J. KLEYWEGT, DICTIONARIES FOR HETEROS, ESF/CCP4 NEWSLETTER 31,JUNE ...Details: TOPOLOGY AND PARAMETER FILES FOR THE TKP-INHIBITOR WERE CREATED USING THE PROGRAM XPLO2D (REF: [O/X-PLOR DICTIONARIES] G.J. KLEYWEGT, DICTIONARIES FOR HETEROS, ESF/CCP4 NEWSLETTER 31,JUNE 1995, PP. 45-50). BOND LENGTHS AND ANGLES ARE FROM IDEALIZED STRUCTURES.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1661 8 %RANDOM
Rwork0.194 ---
obs0.194 21198 100 %-
Displacement parametersBiso mean: 0.276 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 49 68 2766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.78
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.246
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Total num. of bins used: 12 /
Rfactor% reflection
Rfree0.279 -
Rwork0.265 -
obs-100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATOPH11.DNA
X-RAY DIFFRACTION3PARAM.FMNTOPOLOGY.FMN
X-RAY DIFFRACTION4TKP.TOPTKP.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.78
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.246
LS refinement shell
*PLUS
Rfactor obs: 0.265

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