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- PDB-5hi0: The Substrate Binding Mode and Chemical Basis of a Reaction Speci... -

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Basic information

Entry
Database: PDB / ID: 5hi0
TitleThe Substrate Binding Mode and Chemical Basis of a Reaction Specificity Switch in Oxalate Decarboxylase
ComponentsOxalate decarboxylase OxdC
KeywordsLYASE / oxireductase
Function / homology
Function and homology information


oxalate decarboxylase / oxalate decarboxylase activity / oxalate metabolic process / outer membrane-bounded periplasmic space / metal ion binding / cytoplasm
Similarity search - Function
Bicupin, oxalate decarboxylase/oxidase / 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
: / OXALATE ION / Oxalate decarboxylase OxdC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsZhu, W. / Easthon, L.M. / Reinhardt, L.A. / Tu, C. / Cohen, S.E. / Silverman, D.N. / Allen, K.N. / Richards, N.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK061666 United States
CitationJournal: Biochemistry / Year: 2016
Title: Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase.
Authors: Zhu, W. / Easthon, L.M. / Reinhardt, L.A. / Tu, C. / Cohen, S.E. / Silverman, D.N. / Allen, K.N. / Richards, N.G.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 20, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_conn_angle / struct_conn
Item: _entity_poly.pdbx_target_identifier
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxalate decarboxylase OxdC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5505
Polymers44,3211
Non-polymers2294
Water1,874104
1
A: Oxalate decarboxylase OxdC
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)267,29730
Polymers265,9246
Non-polymers1,37324
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_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area46610 Å2
ΔGint-393 kcal/mol
Surface area69770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.619, 154.619, 121.954
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 decarboxylase OxdC


Mass: 44320.656 Da / Num. of mol.: 1 / Mutation: E162 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: oxdC, yvrK, BSU33240 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34714, oxalate decarboxylase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 100 mM Ches, pH 9.5, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9788 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→24.78 Å / Num. obs: 17137 / % possible obs: 98.9 % / Redundancy: 9.8 % / Net I/σ(I): 13.6
Reflection shellHighest resolution: 2.6 Å / Redundancy: 8.2 % / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
SCALAdata scaling
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uw8

1uw8


Resolution: 2.602→24.778 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1712 10 %
Rwork0.1754 --
obs0.1803 17122 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.602→24.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 9 104 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083079
X-RAY DIFFRACTIONf_angle_d1.1054183
X-RAY DIFFRACTIONf_dihedral_angle_d14.0711126
X-RAY DIFFRACTIONf_chiral_restr0.044443
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6025-2.67890.33141290.25481161X-RAY DIFFRACTION90
2.6789-2.76530.3221400.24671255X-RAY DIFFRACTION99
2.7653-2.8640.26781420.21461293X-RAY DIFFRACTION100
2.864-2.97850.28751440.22031286X-RAY DIFFRACTION100
2.9785-3.11380.28091430.17941289X-RAY DIFFRACTION100
3.1138-3.27760.23371430.17971291X-RAY DIFFRACTION100
3.2776-3.48250.24191410.17261271X-RAY DIFFRACTION100
3.4825-3.75050.22761440.16571297X-RAY DIFFRACTION100
3.7505-4.12640.17261440.15421293X-RAY DIFFRACTION100
4.1264-4.71990.19341450.13931304X-RAY DIFFRACTION100
4.7199-5.9330.19121460.16351311X-RAY DIFFRACTION100
5.933-100.19971510.17421359X-RAY DIFFRACTION100

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