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- PDB-2c31: CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE... -

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Basic information

Entry
Database: PDB / ID: 2c31
TitleCRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE COFACTOR DERIVATIVE THIAMIN-2-THIAZOLONE DIPHOSPHATE AND ADENOSINE DIPHOSPHATE
ComponentsOXALYL-COA DECARBOXYLASE
KeywordsLYASE / OXALYL-COA DECARBOXYLASE / OXALATE / THIAMIN DIPHOSPHATE / FLAVOPROTEIN / THIAMINE PYROPHOSPHATE
Function / homology
Function and homology information


oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / oxalate catabolic process / fatty acid alpha-oxidation / thiamine pyrophosphate binding / ADP binding / peroxisome / magnesium ion binding / identical protein binding
Similarity search - Function
Oxalyl-CoA decarboxylase / TPP-binding domain containing protein HACL1-like / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain ...Oxalyl-CoA decarboxylase / TPP-binding domain containing protein HACL1-like / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-TZD / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesOXALOBACTER FORMIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBerthold, C.L. / Moussatche, P. / Richards, N.G.J. / Lindqvist, Y.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structural Basis for Activation of the Thiamin Diphosphate-Dependent Enzyme Oxalyl-Coa Decarboxylase by Adenosine Diphosphate.
Authors: Berthold, C.L. / Moussatche, P. / Richards, N.G.J. / Lindqvist, Y.
#1: Journal: Biochim.Biophys.Acta / Year: 2006
Title: Detection and Characterization of Merohedral Twinning in Crystals of Oxalyl-Coenzyme a Decarboxylase from Oxalobacter Formigenes.
Authors: Berthold, C.L. / Sidhu, H. / Ricagno, S. / Richards, N.G.J. / Lindqvist, Y.
History
DepositionOct 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXALYL-COA DECARBOXYLASE
B: OXALYL-COA DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2838
Polymers121,5002
Non-polymers1,7846
Water11,854658
1
A: OXALYL-COA DECARBOXYLASE
B: OXALYL-COA DECARBOXYLASE
hetero molecules

A: OXALYL-COA DECARBOXYLASE
B: OXALYL-COA DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,56716
Polymers242,9994
Non-polymers3,56712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)124.300, 124.300, 151.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -4.0E-5, 0.00211), (-5.0E-5, -0.99905, -0.04362), (0.00211, -0.04362, 0.99905)
Vector: 117.80213, -0.0752, -0.07706)

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Components

#1: Protein OXALYL-COA DECARBOXYLASE / OXALYL-COENZYME A DECARBOXYLASE


Mass: 60749.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) OXALOBACTER FORMIGENES (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40149, oxalyl-CoA decarboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TZD / 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / THIAMIN THIAZOLONE DIPHOSPHATE


Mass: 440.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O8P2S
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.8 Å3/Da / Density % sol: 53.61 %
Description: ACETOHYDROXYACID SYNTHASE WAS USED AS TEMPLATE TO SOLVE AN APPROXIMATE INCOMPLETE NOT FULLY REFINED STRUCTURE OF OXALYL-COA DECARBOXYLASE IN A DIFFERENT SPACE GROUP TO 4.1 A RESOLUTION. ...Description: ACETOHYDROXYACID SYNTHASE WAS USED AS TEMPLATE TO SOLVE AN APPROXIMATE INCOMPLETE NOT FULLY REFINED STRUCTURE OF OXALYL-COA DECARBOXYLASE IN A DIFFERENT SPACE GROUP TO 4.1 A RESOLUTION. THIS LOW RESOLUTION MODEL WAS THEN USED FOR MOLECULAR REPLACE IN THIS DATA.
Crystal growpH: 6.5
Details: 27V/V % PEG 550MME, 100MM BIS-TRIS PH 6.5, 50MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2004 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 1.73→29.24 Å / Num. obs: 140751 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 21.13 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.9
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JSC

1jsc


Resolution: 1.73→29.2 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: LEAST SQUARES RESIDUAL FOR HEMIHEDRAL TWINNING
Details: THE PROTOCOLL FOR HEMIHEDRALLY TWINNED DATA WAS USED. THE R-VALUES SHOWN IN REMARK 3 ABOVE ARE FOR TWINNED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 12699 4.6 %RANDOM BUT WITH TWIN RELATED REFLECTIONS IN SAME SET
Rwork0.1505 ---
obs0.1505 272696 99.6 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL / Bsol: 56.1554 Å2 / ksol: 0.357619 e/Å3
Displacement parametersBiso mean: 25.19 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å22.18 Å20 Å2
2--2.81 Å20 Å2
3----5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.73→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8157 0 110 658 8925
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006619
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.29298
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.73
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9397
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0521.5
X-RAY DIFFRACTIONc_mcangle_it1.6732
X-RAY DIFFRACTIONc_scbond_it1.8752
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 1.73→1.79 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.278 1219
Rwork0.2523 26176

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