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- PDB-1gox: REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RES... -

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Basic information

Entry
Database: PDB / ID: 1gox
TitleREFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION
Components(S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL
KeywordsOXIDOREDUCTASE (OXYGEN(A))
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 / Glycolate oxidase
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLindqvist, Y.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Refined structure of spinach glycolate oxidase at 2 A resolution.
Authors: Lindqvist, Y.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: The Active Site of Spinach Glycolate Oxidase
Authors: Lindqvist, Y. / Branden, C.-I.
#2: Journal: Eur.J.Biochem. / Year: 1988
Title: Primary Structure of Glycolate Oxidase from Spinach
Authors: Cederlund, E. / Lindqvist, Y. / Soderlund, G. / Branden, C.-I. / Jornvall, H.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Structure of Glycolate Oxidase from Spinach
Authors: Lindqvist, Y. / Branden, C.-I.
#4: Journal: J.Mol.Biol. / Year: 1980
Title: Structure of Glycolate Oxidase from Spinach at a Resolution of 5.5 Angstroms
Authors: Lindqvist, Y. / Branden, C.-I.
#5: Journal: J.Biol.Chem. / Year: 1979
Title: Preliminary Crystallographic Data for Glycolate Oxidase from Spinach
Authors: Lindqvist, Y. / Branden, C.-I.
History
DepositionJun 14, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET PRESENTED AS *BAR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *BAR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8162
Polymers40,3601
Non-polymers4561
Water5,368298
1
A: (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL
hetero molecules

A: (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL
hetero molecules

A: (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL
hetero molecules

A: (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2648
Polymers161,4384
Non-polymers1,8254
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 area16210 Å2
ΔGint-72 kcal/mol
Surface area46750 Å2
MethodPISA, PQS
2
A: (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)326,52716
Polymers322,8768
Non-polymers3,6518
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 area36260 Å2
ΔGint-182 kcal/mol
Surface area89660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.100, 148.100, 135.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-668-

HOH

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Components

#1: Protein (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL


Mass: 40359.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / References: UniProt: P05414, EC: 1.1.3.1
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.59 Å3/Da / Density % sol: 73.19 %
Crystal grow
*PLUS
pH: 8.3 / Method: microdialysis
Details: referred to 'Lindqvist, Y.', (1979) J.Biol.Chem., 254, 7403-7404
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
20.05 MTris-HCl11
35 %(v/v)tertiary butanol12
40.25 mg/mlFMN12
50.05 MTris-HCl12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 70 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.189 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 31 298 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.03
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3121
X-RAY DIFFRACTIONp_mcangle_it1.4521.5
X-RAY DIFFRACTIONp_scbond_it0.8131
X-RAY DIFFRACTIONp_scangle_it1.5211.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1730.15
X-RAY DIFFRACTIONp_singtor_nbd0.1940.5
X-RAY DIFFRACTIONp_multtor_nbd0.20.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2230.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor19.515
X-RAY DIFFRACTIONp_orthonormal_tor27.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5.5 Å / Num. reflection all: 32888 / Rfactor all: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.1 Å2

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