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- PDB-2et1: Oxalate oxidase in complex with substrate analogue glycolate -

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Basic information

Entry
Database: PDB / ID: 2et1
TitleOxalate oxidase in complex with substrate analogue glycolate
ComponentsOxalate oxidase 1
KeywordsOXIDOREDUCTASE / Double stranded beta helix / Cupin
Function / homology
Function and homology information


oxalate oxidase / oxalate oxidase activity / superoxide dismutase complex / apoplast / superoxide dismutase activity / removal of superoxide radicals / cell wall organization / manganese ion binding / identical protein binding
Similarity search - Function
Germin, manganese binding site / Germin family signature. / Germin / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls ...Germin, manganese binding site / Germin family signature. / Germin / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / : / Oxalate oxidase 1
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsRose, R.-S. / Opaleye, O. / Woo, E.-J. / Pickersgill, R.W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and spectroscopic studies shed light on the mechanism of oxalate oxidase
Authors: Opaleye, O. / Rose, R.-S. / Whittaker, M.M. / Woo, E.-J. / Whittaker, J.W. / Pickersgill, R.W.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AUTHOR STATES THAT THE ELECTRON DENSITY SUGGESTS THE FIRST AMINO ACID IS THR RATHER THAN SER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxalate oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3663
Polymers21,2371
Non-polymers1292
Water2,936163
1
A: Oxalate oxidase 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)128,19718
Polymers127,4236
Non-polymers77412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area35330 Å2
ΔGint-278 kcal/mol
Surface area36950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.302, 96.302, 108.133
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Oxalate oxidase 1 / Germin


Mass: 21237.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / References: UniProt: P45850, oxalate oxidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3M ammonium sulfate, 5% 2-propanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 25090 / Num. obs: 24460 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.025 / Rsym value: 0.025 / Net I/σ(I): 40
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 9 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 26 / Num. unique all: 2526 / Rsym value: 0.047 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Oxalate oxidase (pdb entry 1fi2)

1fi2


Resolution: 1.6→12.52 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.304 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1247 5.1 %RANDOM
Rwork0.1766 ---
all0.18 25090 --
obs0.17809 23143 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→12.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 6 163 1660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221530
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.982082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19624.73757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81515240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.489156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021161
X-RAY DIFFRACTIONr_nbd_refined0.2120.2532
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.227
X-RAY DIFFRACTIONr_mcbond_it0.8571.51032
X-RAY DIFFRACTIONr_mcangle_it1.18621618
X-RAY DIFFRACTIONr_scbond_it2.1063556
X-RAY DIFFRACTIONr_scangle_it3.1184.5464
LS refinement shellResolution: 1.6→1.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 100 -
Rwork0.17 1658 -
obs--100 %

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