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- PDB-8rio: Beta-keto acid cleavage enzyme from Paracoccus denitrificans -

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Basic information

Entry
Database: PDB / ID: 8rio
TitleBeta-keto acid cleavage enzyme from Paracoccus denitrificans
Components3-keto-5-aminohexanoate cleavage protein
KeywordsLYASE / aldolase / BKACE
Function / homology3-keto-5-aminohexanoate cleavage activity / 3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase-type TIM barrel / metal ion binding / PROLINE / 3-keto-5-aminohexanoate cleavage protein
Function and homology information
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMarchal, D.G. / Zarzycki, J. / Erb, T.J.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
European Commission862087European Union
CitationJournal: Nat Commun / Year: 2025
Title: Design and implementation of aerobic and ambient CO 2 -reduction as an entry-point for enhanced carbon fixation.
Authors: Satanowski, A. / Marchal, D.G. / Perret, A. / Petit, J.L. / Bouzon, M. / Doring, V. / Dubois, I. / He, H. / Smith, E.N. / Pellouin, V. / Petri, H.M. / Rainaldi, V. / Nattermann, M. / ...Authors: Satanowski, A. / Marchal, D.G. / Perret, A. / Petit, J.L. / Bouzon, M. / Doring, V. / Dubois, I. / He, H. / Smith, E.N. / Pellouin, V. / Petri, H.M. / Rainaldi, V. / Nattermann, M. / Burgener, S. / Paczia, N. / Zarzycki, J. / Heinemann, M. / Bar-Even, A. / Erb, T.J.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-keto-5-aminohexanoate cleavage protein
B: 3-keto-5-aminohexanoate cleavage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5476
Polymers67,1862
Non-polymers3614
Water14,808822
1
A: 3-keto-5-aminohexanoate cleavage protein
B: 3-keto-5-aminohexanoate cleavage protein
hetero molecules

A: 3-keto-5-aminohexanoate cleavage protein
B: 3-keto-5-aminohexanoate cleavage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,09512
Polymers134,3724
Non-polymers7228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9210 Å2
ΔGint-37 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.065, 137.871, 132.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-506-

HOH

21B-553-

HOH

31B-587-

HOH

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Components

#1: Protein 3-keto-5-aminohexanoate cleavage protein


Mass: 33593.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans PD1222 (bacteria)
Gene: Pden_3578 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1B802
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The enzyme (8.6 mg/mL) in 50 mM HEPES pH 7.8, 150 mM KCl, 1 M L-proline, and 1 mM ZnCl2 was mixed in a 1:1 ratio with 25 % (w/v) pentaerythritol propoxylate (17/8 PO/OH), 100 mM HEPES pH 7.5. ...Details: The enzyme (8.6 mg/mL) in 50 mM HEPES pH 7.8, 150 mM KCl, 1 M L-proline, and 1 mM ZnCl2 was mixed in a 1:1 ratio with 25 % (w/v) pentaerythritol propoxylate (17/8 PO/OH), 100 mM HEPES pH 7.5. The final size of the drops was 1 microliter. Prior to flash freezing the crystals in liquid nitrogen, the mother liquor was supplemented with 37 % (w/v) pentaerythrol propoxylate (17/8 PO/OH).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Aug 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→24.78 Å / Num. obs: 129609 / % possible obs: 99.1 % / Redundancy: 12.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.026 / Rrim(I) all: 0.093 / Net I/σ(I): 19.2 / Num. measured all: 1572792
Reflection shellResolution: 1.45→1.53 Å / % possible obs: 95.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.499 / Num. measured all: 194961 / Num. unique obs: 18038 / CC1/2: 0.929 / Rpim(I) all: 0.157 / Rrim(I) all: 0.525 / Net I/σ(I) obs: 5.9

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Processing

Software
NameVersionClassification
XDS20210323data reduction
SCALA3.3.22data scaling
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→24.78 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 2005 1.55 %
Rwork0.1564 --
obs0.1567 129520 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 18 822 5532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154839
X-RAY DIFFRACTIONf_angle_d1.4256563
X-RAY DIFFRACTIONf_dihedral_angle_d12.6861759
X-RAY DIFFRACTIONf_chiral_restr0.113719
X-RAY DIFFRACTIONf_plane_restr0.014874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.2621270.23078314X-RAY DIFFRACTION91
1.49-1.530.19451450.18378996X-RAY DIFFRACTION99
1.53-1.570.19691400.1769082X-RAY DIFFRACTION99
1.57-1.620.21191400.16549102X-RAY DIFFRACTION99
1.62-1.680.21241420.15819051X-RAY DIFFRACTION99
1.68-1.750.16061490.15249095X-RAY DIFFRACTION99
1.75-1.830.22341420.15769103X-RAY DIFFRACTION99
1.83-1.920.19111460.15859176X-RAY DIFFRACTION100
1.92-2.040.1511410.15059156X-RAY DIFFRACTION100
2.04-2.20.17311450.14549156X-RAY DIFFRACTION100
2.2-2.420.17951480.15069206X-RAY DIFFRACTION100
2.42-2.770.171420.15739236X-RAY DIFFRACTION100
2.77-3.490.14291460.15889305X-RAY DIFFRACTION100
3.49-24.780.18181520.14939537X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.343 Å / Origin y: -13.6246 Å / Origin z: -10.274 Å
111213212223313233
T0.1399 Å20.0054 Å2-0.008 Å2-0.1115 Å20.0005 Å2--0.096 Å2
L0.457 °20.0585 °2-0.0853 °2-0.1134 °20.0035 °2--0.1931 °2
S-0.0029 Å °0.0302 Å °-0.0394 Å °-0.0041 Å °0.0007 Å °0.003 Å °0.0175 Å °0.001 Å °0.0021 Å °
Refinement TLS groupSelection details: all

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