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- PDB-7b2e: quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum e... -

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Basic information

Entry
Database: PDB / ID: 7b2e
Titlequadruple mutant of oxalyl-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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 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

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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)500,47732
Polymers493,4638
Non-polymers7,01524
Water22,9151272
1
A: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
B: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
F: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
G: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,23916
Polymers246,7314
Non-polymers3,50712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29580 Å2
ΔGint-202 kcal/mol
Surface area63350 Å2
MethodPISA
2
C: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
D: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
E: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
H: Putative oxalyl-CoA decarboxylase (Oxc, yfdU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,23916
Polymers246,7314
Non-polymers3,50712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29550 Å2
ΔGint-198 kcal/mol
Surface area63290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.094, 180.337, 202.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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: 61682.863 Da / Num. of mol.: 8 / Mutation: E135G, A415C, Y497F, S568G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / 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 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: reservoir: 25% w/v pentaerythriol propoxylate (17/8 PO/OH), 100 mM Tris pH 8.5, 50 mM Magnesium chloride condition: 10% w/v pentaerythriol propoxylate (17/8 PO/OH), 40 mM Tris pH 8.5, 30 mM ...Details: reservoir: 25% w/v pentaerythriol propoxylate (17/8 PO/OH), 100 mM Tris pH 8.5, 50 mM Magnesium chloride condition: 10% w/v pentaerythriol propoxylate (17/8 PO/OH), 40 mM Tris pH 8.5, 30 mM Magnesium chloride, 4 mg/mL Protein, 10 mM HEPES-KOH pH 7.8, 30 mM NaCl, 2 mM TPP, 1 mM CoA
PH range: 7.8-8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream (liquid nitrogen) / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→29.941 Å / Num. obs: 144506 / % possible obs: 99.8 % / Redundancy: 13.6 % / CC1/2: 0.997 / Rpim(I) all: 0.074 / Rrim(I) all: 0.277 / Rsym value: 0.266 / Net I/av σ(I): 2.4 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.8-2.95140.8290.8208240.9760.2270.860.82999.4
2.95-3.13140.591.1197850.1620.6120.5999.9
3.13-3.3513.80.441.5186890.1220.4570.4499.9
3.35-3.6212.90.322173970.0920.3330.3299.9
3.62-3.96140.2382.7160440.0660.2470.23899.9
3.96-4.43140.1793.5145400.050.1860.17999.9
4.43-5.1113.20.1544128860.0440.160.154100
5.11-6.2613.30.1913.3109770.0540.1990.191100
6.26-8.8613.40.122585920.0350.1270.122100
8.86-29.941120.0687.547720.0210.0720.06897.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XDSBUILT=20200417data reduction
pointless1.12.1data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AYG

7ayg


Resolution: 2.8→29.94 Å / SU ML: 0.2819 / Cross valid method: FREE R-VALUE / σ(F): 0.76 / Phase error: 30.4356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 1996 1.39 %
Rwork0.2018 141872 -
obs0.2022 143868 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32512 0 432 1272 34216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002333584
X-RAY DIFFRACTIONf_angle_d0.559345642
X-RAY DIFFRACTIONf_chiral_restr0.04525232
X-RAY DIFFRACTIONf_plane_restr0.00395930
X-RAY DIFFRACTIONf_dihedral_angle_d21.927112338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.33231390.27259941X-RAY DIFFRACTION98.65
2.87-2.950.32281410.251310067X-RAY DIFFRACTION99.68
2.95-3.030.28481420.239310061X-RAY DIFFRACTION99.77
3.03-3.130.28011410.230110022X-RAY DIFFRACTION99.47
3.13-3.240.25761420.226910089X-RAY DIFFRACTION99.51
3.24-3.370.27011420.214610036X-RAY DIFFRACTION99.39
3.37-3.530.24461420.207510075X-RAY DIFFRACTION99.5
3.53-3.710.23771430.198810110X-RAY DIFFRACTION99.69
3.71-3.950.23421420.183410128X-RAY DIFFRACTION99.57
3.95-4.250.18241420.176810162X-RAY DIFFRACTION99.64
4.25-4.680.18031430.16310172X-RAY DIFFRACTION99.7
4.68-5.350.18241440.181210234X-RAY DIFFRACTION99.77
5.35-6.730.22261460.206210319X-RAY DIFFRACTION99.84
6.73-29.940.20131470.182710456X-RAY DIFFRACTION98.53
Refinement TLS params.Method: refined / Origin x: -5.82337183126 Å / Origin y: -90.0796928759 Å / Origin z: 0.0183502455143 Å
111213212223313233
T0.206794033433 Å2-0.00447802827803 Å20.00465856909979 Å2-0.293874121419 Å20.00429237490129 Å2--0.209424288901 Å2
L0.0055443435956 °2-0.0178139247732 °2-0.00169452490209 °2-0.141157905376 °20.0484405363464 °2--0.018472380246 °2
S-0.00110218384249 Å °0.0101023999582 Å °-0.000407143080402 Å °-0.00716963410773 Å °0.00898278721728 Å °-0.00648452509651 Å °-0.00494028030944 Å °0.00639941239924 Å °-0.00832681447233 Å °
Refinement TLS groupSelection details: all

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