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- PDB-2ji7: X-ray structure of Oxalyl-CoA decarboxylase with covalent reactio... -

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Basic information

Entry
Database: PDB / ID: 2ji7
TitleX-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate
ComponentsOXALYL-COA DECARBOXYLASE
KeywordsLYASE / FLAVOPROTEIN / DECARBOXYLASE / OXALATE DEGRADATION / INTERMEDIATE COMPLEX / THIAMIN DIPHOSPHATE-DEPENDENT / THIAMINE PYROPHOSPHATE / NON- OXIDATIVE DECARBOXYLASE
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 / 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-OXT / TRIETHYLENE GLYCOL / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesOXALOBACTER FORMIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBerthold, C.L. / Toyota, C.G. / Moussatche, P. / Wood, M.D. / Leeper, F. / Richards, N.G.J. / Lindqvist, Y.
CitationJournal: Structure / Year: 2007
Title: Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases
Authors: Berthold, C.L. / Toyota, C.G. / Moussatche, P. / Wood, M.D. / Leeper, F. / Richards, N.G.J. / Lindqvist, Y.
History
DepositionFeb 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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)126,83916
Polymers121,5002
Non-polymers5,33914
Water21,3481185
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)253,67832
Polymers242,9994
Non-polymers10,67828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area29720 Å2
ΔGint-172.8 kcal/mol
Surface area79790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)126.181, 126.181, 151.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2184-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.002592, 0.000765), (-0.002636, -0.998, -0.06383), (0.000598, -0.06383, 0.998)
Vector: 119.5, -1.458, -0.07888)

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Components

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Protein , 1 types, 2 molecules AB

#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) / Plasmid: PET9A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40149, oxalyl-CoA decarboxylase

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Non-polymers , 6 types, 1199 molecules

#2: Chemical ChemComp-OXT / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1R,11R,15S,17R)-19-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-1,11,15,17-TETRAHYDROXY-12,12-DIMETHYL-15,17-DIOXIDO-6,10-DIOXO-14,16,18-TRIOXA-2-THIA-5,9-DIAZA-15,17-DIPHOSPHANONADEC-1-YL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM


Mass: 1220.859 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H55N11O24P5S2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1185 / 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: 2.9 Å3/Da / Density % sol: 57.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 9, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: THIN DIAMOND DOUBLE CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.82→76 Å / Num. obs: 124184 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C31

2c31


Resolution: 1.82→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.325 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 5831 4.7 %RANDOM
Rwork0.15 ---
obs0.151 118269 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.59 Å20 Å2
2--1.17 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.82→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 0 342 1185 9875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228949
X-RAY DIFFRACTIONr_bond_other_d0.010.026057
X-RAY DIFFRACTIONr_angle_refined_deg1.4252.01512161
X-RAY DIFFRACTIONr_angle_other_deg1.6223.00514718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64151152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74924.839341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.422151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2621548
X-RAY DIFFRACTIONr_chiral_restr0.1380.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021614
X-RAY DIFFRACTIONr_nbd_refined0.20.21888
X-RAY DIFFRACTIONr_nbd_other0.1810.26475
X-RAY DIFFRACTIONr_nbtor_refined0.1670.24381
X-RAY DIFFRACTIONr_nbtor_other0.0850.24327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2960
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.80435835
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08648972
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.22243630
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.82453171
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 409
Rwork0.273 8732
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1231-0.138-0.04720.5090.08860.85190.0064-0.0248-0.02490.0711-0.0155-0.00620.12170.01320.0091-0.1473-0.04020.0106-0.134-0.0028-0.136663.5119-17.6365-5.088
20.2232-0.14370.02030.6588-0.03680.72480.0162-0.03780.03330.073-0.02060.0641-0.0835-0.1250.0044-0.1582-0.00730.0059-0.1131-0.0324-0.135756.042216.3163-4.0054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 565
2X-RAY DIFFRACTION2B7 - 565

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