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- PDB-2q29: Crystal structure of oxalyl-coA decarboxylase from Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 2q29
TitleCrystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with acetyl coenzyme A
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 / 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
ACETYL COENZYME *A / THIAMINE DIPHOSPHATE / Oxalyl-CoA decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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)124,18710
Polymers121,2782
Non-polymers2,9098
Water11,908661
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)248,37420
Polymers242,5564
Non-polymers5,81816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area30170 Å2
ΔGint-176 kcal/mol
Surface area63970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.570, 145.530, 147.190
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-4200-

HOH

21A-4282-

HOH

31B-4253-

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 , 5 types, 669 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% PEG4000, 0.2M sodium acetate. 0.0025M thiamine diphosphate, 0.0025M magnesium sulfate, 0.001M acetyl coenzyme A, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9785 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Feb 16, 2007
RadiationMonochromator: Fixed exit double crystal Si [111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.82→99 Å / Num. obs: 126889 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.052 / Χ2: 1.003 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.82-1.856.70.25762630.94899.9
1.85-1.897.10.22763020.923100
1.89-1.927.10.19362860.952100
1.92-1.967.20.15862670.954100
1.96-27.20.1463150.956100
2-2.057.20.12663240.976100
2.05-2.17.20.1162710.989100
2.1-2.167.20.163201.009100
2.16-2.227.20.09362841.032100
2.22-2.297.20.08463401.043100
2.29-2.387.30.07763041.044100
2.38-2.477.30.07263231.044100
2.47-2.587.30.06563521.045100
2.58-2.727.30.0663401.041100
2.72-2.897.30.05563591.043100
2.89-3.117.30.0563521.042100
3.11-3.437.30.04363731.032100
3.43-3.927.30.03764161.018100
3.92-4.947.30.03164590.995100
4.94-997.10.03266390.96699.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å46.49 Å
Translation1.97 Å46.49 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: 1.82→42.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.009 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1275 1 %RANDOM
Rwork0.175 ---
obs0.175 126549 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.584 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.82→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8236 0 140 661 9037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228530
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.98411614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68451090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61124.576354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.434151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4541552
X-RAY DIFFRACTIONr_chiral_restr0.1020.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026416
X-RAY DIFFRACTIONr_nbd_refined0.20.24159
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2637
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.2158
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.263
X-RAY DIFFRACTIONr_mcbond_it0.8261.55597
X-RAY DIFFRACTIONr_mcangle_it1.26128710
X-RAY DIFFRACTIONr_scbond_it2.20733326
X-RAY DIFFRACTIONr_scangle_it3.5494.52904
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 90 -
Rwork0.232 9178 -
obs-9268 99.67 %

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