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- PDB-2jib: X-ray structure of Oxalyl-CoA decarboxylase in complex with coenz... -

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Basic information

Entry
Database: PDB / ID: 2jib
TitleX-ray structure of Oxalyl-CoA decarboxylase in complex with coenzyme- A
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 / 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 / COENZYME A / TRIETHYLENE GLYCOL / THIAMINE DIPHOSPHATE / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesOXALOBACTER FORMIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)125,08912
Polymers121,5002
Non-polymers3,58910
Water11,998666
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)250,17824
Polymers242,9994
Non-polymers7,17820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area28550 Å2
ΔGint-171.4 kcal/mol
Surface area77830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.662, 127.662, 152.074
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: (0.000891, 0.00074), (-0.997, 0.07779, 0.000836), (0.07779, 0.997)
Vector: 134.5, 1.939, -0.1518)

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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, 676 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: May 6, 2006 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→63.89 Å / Num. obs: 72341 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.8 / % possible all: 99.4

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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: 2.2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.33 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3439 4.8 %RANDOM
Rwork0.199 ---
obs0.201 68821 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å22.09 Å20 Å2
2--4.17 Å20 Å2
3----6.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 0 224 666 9238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228786
X-RAY DIFFRACTIONr_bond_other_d0.0010.025889
X-RAY DIFFRACTIONr_angle_refined_deg1.1692.00311933
X-RAY DIFFRACTIONr_angle_other_deg0.861314466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66151134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4124.824340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1151475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.721548
X-RAY DIFFRACTIONr_chiral_restr0.0650.21325
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021599
X-RAY DIFFRACTIONr_nbd_refined0.1880.21999
X-RAY DIFFRACTIONr_nbd_other0.180.26367
X-RAY DIFFRACTIONr_nbtor_refined0.1660.24333
X-RAY DIFFRACTIONr_nbtor_other0.0840.24323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2634
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.331.57216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39328920
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.74233701
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0724.53004
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.385 237
Rwork0.31 5050
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)
10.2192-0.18590.01840.913-0.22411.6507-0.0214-0.0177-0.02670.1514-0.0296-0.04310.16380.29080.051-0.19640.00520.00050.01110.0219-0.102370.9073-16.2124-3.896
20.122-0.25010.02690.8084-0.29651.7999-0.01670.03740.00190.2426-0.0042-0.0012-0.31250.0090.0209-0.1678-0.0658-0.0153-0.0565-0.0082-0.080463.537217.8493-5.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 565
2X-RAY DIFFRACTION2B7 - 565

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