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- PDB-2q28: Crystal structure of oxalyl-coA decarboxylase from Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 2q28
TitleCrystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with adenosine-5`-diphosphate
Componentsoxalyl-CoA decarboxylase
KeywordsLYASE / OXALYL-COA DECARBOXYLASE / OXALATE DEGRADATION / THIAMINE DIPHOSPHATE
Function / homology
Function and homology information


oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / oxalate catabolic process / fatty acid alpha-oxidation / cellular response to acidic pH / 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 / THIAMINE DIPHOSPHATE / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWerther, T. / Zimmer, A. / Wille, G. / Hubner, G. / Weiss, M.S. / Konig, S.
CitationJournal: Febs J. / Year: 2010
Title: New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli.
Authors: Werther, T. / Zimmer, A. / Wille, G. / Golbik, R. / Weiss, M.S. / Konig, S.
History
DepositionMay 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)123,86216
Polymers121,2782
Non-polymers2,58514
Water16,069892
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)247,72532
Polymers242,5564
Non-polymers5,16928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area34360 Å2
ΔGint-231 kcal/mol
Surface area64850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.270, 143.620, 147.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-4250-

HOH

21A-4342-

HOH

DetailsThe biological assembly is a tetramer (dimer of dimers) generated from dimer in the asymmetric unit by the operations: -x, y, -1/2-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein oxalyl-CoA decarboxylase


Mass: 60638.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: yfdU / Plasmid: pMS470-115/6/5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AFI0, oxalyl-CoA decarboxylase

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Non-polymers , 7 types, 906 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: 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
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.75M ammonium sulfate, 0.005M adenosine diphosphate, 0.0025M thiamine diphosphate, 0.0025 mM magnesium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.93001 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Dec 7, 2006
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93001 Å / Relative weight: 1
ReflectionResolution: 1.74→99 Å / Num. obs: 143107 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.104 / Χ2: 1.041 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.74-1.776.80.86770850.971100
1.77-1.86.80.76171110.967100
1.8-1.846.90.65870750.987100
1.84-1.876.90.5870961.007100
1.87-1.9270.49571391.029100
1.92-1.9670.38670941.048100
1.96-2.017.10.3471101.037100
2.01-2.067.20.27571101.061100
2.06-2.127.20.23271311.064100
2.12-2.197.20.20370921.05100
2.19-2.277.30.17971881.08100
2.27-2.367.30.15371331.068100
2.36-2.477.30.13671251.059100
2.47-2.67.30.11771541.073100
2.6-2.767.30.1171661.084100
2.76-2.987.30.10471731.107100
2.98-3.277.30.09572121.124100
3.27-3.757.30.07672341.087100
3.75-4.727.30.04372730.998100
4.72-997.10.02874060.89698.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.91 Å21.56 Å
Translation1.91 Å21.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→20.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.836 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1436 1 %RANDOM
Rwork0.177 ---
obs0.178 142512 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.11 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.74→20.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8294 0 158 892 9344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228602
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.98311702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57151098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26924.551356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.541151390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2941552
X-RAY DIFFRACTIONr_chiral_restr0.0870.21336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026462
X-RAY DIFFRACTIONr_nbd_refined0.2010.24368
X-RAY DIFFRACTIONr_nbtor_refined0.3060.26004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2772
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.2160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.268
X-RAY DIFFRACTIONr_mcbond_it0.7421.55607
X-RAY DIFFRACTIONr_mcangle_it1.18428772
X-RAY DIFFRACTIONr_scbond_it2.05233367
X-RAY DIFFRACTIONr_scangle_it3.2724.52930
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 132 -
Rwork0.243 10275 -
obs-10407 99.68 %

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