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- PDB-7ayg: oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound... -

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Basic information

Entry
Database: PDB / ID: 7ayg
Titleoxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP
ComponentsPutative oxalyl-CoA decarboxylase (Oxc, yfdU)
KeywordsLYASE / Decarboxylase / Carboxylase / Ligase / Formyl-CoA / Oxalyl-CoA / Mandelyl-CoA
Function / homology
Function and homology information


oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / oxalate catabolic process / thiamine pyrophosphate binding / magnesium ion 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-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / THIAMINE DIPHOSPHATE / Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPfister, P. / Burgener, S. / Nattermann, M. / Zarzycki, J. / Erb, T.J.
Funding support Germany, United States, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFormatPlant Germany
Department of Energy (DOE, United States)DE-EE0008499 United States
Citation
Journal: Acs Catalysis / Year: 2021
Title: Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism.
Authors: Nattermann, M. / Burgener, S. / Pfister, P. / Chou, A. / Schulz, L. / Lee, S.H. / Paczia, N. / Zarzycki, J. / Gonzalez, R. / Erb, T.J.
History
DepositionNov 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 13, 2021Group: Data collection / Database references / Category: citation_author / pdbx_database_proc / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
B: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
C: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
D: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
E: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
F: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
G: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
H: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)501,16632
Polymers494,1518
Non-polymers7,01524
Water70,4393910
1
A: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
B: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
C: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
D: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,58316
Polymers247,0764
Non-polymers3,50712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29420 Å2
ΔGint-203 kcal/mol
Surface area63420 Å2
MethodPISA
2
E: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
F: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
G: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
H: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,58316
Polymers247,0764
Non-polymers3,50712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29390 Å2
ΔGint-203 kcal/mol
Surface area63620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.176, 181.798, 202.366
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Putative oxalyl-CoA decarboxylase (Oxc, yfdU)


Mass: 61768.895 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Gene: MexAM1_META1p0990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5AX46, oxalyl-CoA decarboxylase
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3910 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 45 % w/v Pentaerythritol ethoxylate (3/4 EO/OH), 100 mM Sodium acetate pH 4.6, 400 mM Potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.9→39.3 Å / Num. obs: 455609 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Rrim(I) all: 0.118 / Rsym value: 0.107 / Net I/av σ(I): 4.7 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-25.40.8250.9355003655770.3860.9150.8252.298.3
2-2.125.80.5231.4367487628700.2350.5740.5233.499.5
2.12-2.275.80.3122.3342631590870.1420.3440.312599.4
2.27-2.455.60.2043.4307932551600.0950.2260.2046.599.5
2.45-2.695.70.1414.7286033502710.0650.1550.1418.698.5
2.69-35.90.1115.6272925461510.050.1230.11110.799.7
3-3.475.60.0816.7229901407650.0370.090.08114.499.6
3.47-4.255.60.0627.9191304340330.0290.0690.06218.698.1
4.25-6.015.80.0558.3155252269980.0250.060.05520.599.8
6.01-39.1075.60.0489.282630146970.0220.0530.04820.596.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSBUILT20200417data reduction
XSCALEBUILT20200417data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ji6

2ji6


Resolution: 1.9→39.3 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 1987 0.44 %
Rwork0.1765 452238 -
obs0.1766 454225 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.09 Å2 / Biso mean: 27.8543 Å2 / Biso min: 17.76 Å2
Refinement stepCycle: final / Resolution: 1.9→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32464 0 432 3910 36806
Biso mean--22.51 35.41 -
Num. residues----4368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.36111390.3468315293166897
1.95-20.30261400.2788321233226399
2-2.060.25841430.2371322013234499
2.06-2.130.25531400.217322803242099
2.13-2.20.25561430.2096322333237699
2.2-2.290.23111420.2009322753241799
2.29-2.390.21771420.1763324213256399
2.39-2.520.20491380.1758317173185597
2.52-2.680.19351420.1702324963263899
2.68-2.880.231430.1764325563269999
2.88-3.170.23071440.1726325903273499
3.17-3.630.17841420.161321173225998
3.63-4.580.16181460.1351328623300899
4.58-39.110.16931430.1504328383298197
Refinement TLS params.Method: refined / Origin x: -5.6047 Å / Origin y: 90.8763 Å / Origin z: 0.0076 Å
111213212223313233
T0.1958 Å2-0.0042 Å2-0.0026 Å2-0.2914 Å2-0.0006 Å2--0.1945 Å2
L0.0166 °2-0.0095 °2-0.01 °2-0.0643 °20.025 °2--0.0201 °2
S-0.0042 Å °0.023 Å °-0.0014 Å °-0.0026 Å °0.0123 Å °0.0006 Å °-0.0034 Å °0.0115 Å °-0.0083 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA22 - 603
2X-RAY DIFFRACTION1allB22 - 603
3X-RAY DIFFRACTION1allC22 - 603
4X-RAY DIFFRACTION1allD22 - 603
5X-RAY DIFFRACTION1allE22 - 603
6X-RAY DIFFRACTION1allF22 - 603
7X-RAY DIFFRACTION1allG22 - 603
8X-RAY DIFFRACTION1allH22 - 603
9X-RAY DIFFRACTION1allS1 - 3910

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