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- PDB-1gyl: INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRAT... -

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Basic information

Entry
Database: PDB / ID: 1gyl
TitleINVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE
ComponentsGLYCOLATE OXIDASE
KeywordsOXIDOREDUCTASE (FLAVOENZYME)
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: 3 Å
AuthorsLindqvist, Y. / Stenberg, K.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.
Authors: Stenberg, K. / Clausen, T. / Lindqvist, Y. / Macheroux, P.
#1: Journal: Eur.J.Biochem. / Year: 1993
Title: Role of Tyrosine 129 in the Active Site of Spinach Glycolate Oxidase
Authors: Macheroux, P. / Kieweg, V. / Massey, V. / Soderlind, E. / Stenberg, K. / Lindqvist, Y.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: The Active Site of Spinach Glycolate Oxidase
Authors: Lindqvist, Y. / Branden, C.-I.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Refined Structure of Spinach Glycolate Oxidase at 2 Angstroms Resolution
Authors: Lindqvist, Y.
History
DepositionJan 30, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_ref_seq_dif / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: GLYCOLATE OXIDASE
B: GLYCOLATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0913
Polymers80,6352
Non-polymers4561
Water362
1
A: GLYCOLATE OXIDASE
B: GLYCOLATE OXIDASE
hetero molecules

A: GLYCOLATE OXIDASE
B: GLYCOLATE OXIDASE
hetero molecules

A: GLYCOLATE OXIDASE
B: GLYCOLATE OXIDASE
hetero molecules

A: GLYCOLATE OXIDASE
B: GLYCOLATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,36512
Polymers322,5408
Non-polymers1,8254
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)145.500, 145.500, 100.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-1), (-1), (-1) / Vector: 73, 71.5, 48.5)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 359 B 1 .. B 359 2.2

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Components

#1: Protein GLYCOLATE OXIDASE


Mass: 40317.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: GLYCOLATE OXIDASE FROM SPINACH / Plasmid: PKS26 / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Source detailsPET-BASED EXPRESSION SYSTEM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21 Msodium acetate1reservoir
30.4 %octyl pyranoside1reservoir
4100 mMimidazol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 18421 / % possible obs: 82.7 %
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 54.6 Å / Num. measured all: 41999 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 71.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 3 Å /
RfactorNum. reflection
Rwork0.254 -
obs0.254 41999
Displacement parametersBiso mean: 15.7 Å2
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5405 0 31 2 5438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Lowest resolution: 6.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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