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- PDB-2ji6: X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-dea... -

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Basic information

Entry
Database: PDB / ID: 2ji6
TitleX-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP and oxalyl-CoA
ComponentsOXALYL-COA DECARBOXYLASE
KeywordsLYASE / FLAVOPROTEIN / DECARBOXYLASE / THIAMIN DIPHOSPHATE-DEPENDENT / SUBSTRATE COMPLEX / OXALATE DEGRADATION / 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 / 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 / OXALYL-COENZYME A / TRIETHYLENE GLYCOL / Chem-TPW / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesOXALOBACTER FORMIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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)125,79414
Polymers121,5002
Non-polymers4,29412
Water16,358908
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)251,58728
Polymers242,9994
Non-polymers8,58824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area28380 Å2
ΔGint-171.6 kcal/mol
Surface area77380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.002, 127.002, 151.813
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, 0.001919, -0.000965), (-0.001839, -0.9971, -0.07672), (-0.001109, -0.07672, 0.9971)
Vector: 120.1, -1.825, -0.00512)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein OXALYL-COA DECARBOXYLASE / OXALYL-COENZYMEA 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 , 7 types, 920 molecules

#2: Chemical ChemComp-TPW / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / 3-DEAZA-THDP


Mass: 423.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N3O7P2S
#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-OXK / OXALYL-COENZYME A


Mass: 839.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H36N7O19P3S
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: 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.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 58 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.083
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 19, 2006 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR
RadiationMonochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.083 Å / Relative weight: 1
ReflectionResolution: 2.06→152 Å / Num. obs: 84850 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 24.88 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 74.2

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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: 2.06→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.892 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3994 4.7 %RANDOM
Rwork0.174 ---
obs0.176 80775 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å21.46 Å20 Å2
2--2.91 Å20 Å2
3----4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 0 272 908 9528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228878
X-RAY DIFFRACTIONr_bond_other_d0.0010.025957
X-RAY DIFFRACTIONr_angle_refined_deg1.3882.00612067
X-RAY DIFFRACTIONr_angle_other_deg0.9053.00114585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76151148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66924.855344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.939151486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7521548
X-RAY DIFFRACTIONr_chiral_restr0.1190.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021614
X-RAY DIFFRACTIONr_nbd_refined0.1920.21988
X-RAY DIFFRACTIONr_nbd_other0.1840.26517
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24365
X-RAY DIFFRACTIONr_nbtor_other0.0850.24412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2829
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.10737260
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32348966
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.48643788
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.89753086
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: 2.07→2.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 230
Rwork0.273 4789
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)
10.0894-0.2034-0.03720.87850.35531.56170.00110.04950.01740.1407-0.0226-0.02660.2377-0.01480.0215-0.1765-0.0680.0054-0.08270.0084-0.134163.7937-17.7597-5.1947
20.2174-0.1219-0.03630.96070.00821.43430.00710.01020.01360.1229-0.03450.0497-0.1892-0.26320.0274-0.19410.00680.0058-0.0491-0.0336-0.129956.390516.18-3.8966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 565
2X-RAY DIFFRACTION2B7 - 565

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