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- PDB-1al7: THREE-DIMENSIONAL STRUCTURES OF GLYCOLATE OXIDASE WITH BOUND ACTI... -

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Basic information

Entry
Database: PDB / ID: 1al7
TitleTHREE-DIMENSIONAL STRUCTURES 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
FLAVIN MONONUCLEOTIDE / Chem-HST / Glycolate oxidase
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.6 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 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)40,0923
Polymers39,3361
Non-polymers7562
Water5,260292
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)160,36912
Polymers157,3454
Non-polymers3,0238
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 area18100 Å2
ΔGint-36 kcal/mol
Surface area45970 Å2
MethodPISA, PQS
2
A: GLYCOLATE OXIDASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)320,73724
Polymers314,6918
Non-polymers6,04616
Water1448
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
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area39360 Å2
ΔGint-100 kcal/mol
Surface area88780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.100, 148.100, 136.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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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: GLYCOLATE OXIDASE COMPLEXED 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-HST / 4-CARBOXY-5-(1-PENTYL)HEXYLSULFANYL-1,2,3-TRIAZOLE


Mass: 299.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 4.76 Å3/Da / Density % sol: 74.13 %
Crystal growpH: 8.3
Details: PROTEIN WAS CRYSTALLISED FROM 50MM TRIS-BUFFER PH 8.3, 0.25 MG/ML FMN, 4% TERTIARY BUTANOL, SATURATED WITH THE INHIBITOR.
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

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 20291 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.99
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.206 / % possible all: 74.4
Reflection
*PLUS
Num. measured all: 48698
Reflection shell
*PLUS
% possible obs: 74.4 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.6→8 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: TOPOLOGY AND PARAMETER FILES FOR THE TKCA-INHIBITOR WERE CREATED USING THE PROGRAMME XPLO2D (REF: [O/X-PLOR DICTIONARIES] G.J. KLEYWEGT, DICTIONARIES FOR HETEROS, ESF/CCP4 NEWSLETTER 31,JUNE ...Details: TOPOLOGY AND PARAMETER FILES FOR THE TKCA-INHIBITOR WERE CREATED USING THE PROGRAMME 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
Rfree0.242 1579 8 %RANDOM
Rwork0.18 ---
obs0.18 20005 87.1 %-
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 51 292 3040
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_deg1.374
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.95
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
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: 2.68→2.76 Å / Total num. of bins used: 12 /
Rfactor% reflection
Rfree0.357 -
Rwork0.258 -
obs-74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATOPH11.DNA
X-RAY DIFFRACTION3PARAM.FMNTOPOLOGY.FMN
X-RAY DIFFRACTION4TACA.TOPTACA.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.952
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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