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- PDB-8rip: Beta-keto acid cleavage enzyme from Paracoccus denitrificans with... -

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Basic information

Entry
Database: PDB / ID: 8rip
TitleBeta-keto acid cleavage enzyme from Paracoccus denitrificans with bound malonate and Coenzyme A
Components3-keto-5-aminohexanoate cleavage protein
KeywordsLYASE / aldolase / CoA / coenzyme A / 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 / COENZYME A / MALONATE ION / 3-keto-5-aminohexanoate cleavage protein
Function and homology information
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
C: 3-keto-5-aminohexanoate cleavage protein
D: 3-keto-5-aminohexanoate cleavage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,91714
Polymers145,7134
Non-polymers2,20510
Water16,502916
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-182 kcal/mol
Surface area39930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.155, 134.350, 140.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36428.133 Da / Num. of mol.: 4
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
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 20 % w/v PEG3350, 200 mM di-sodium malonate pH 7.0. The final size of ...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 20 % w/v PEG3350, 200 mM di-sodium malonate pH 7.0. The final size of the drops was 1 microliter. Prior to flash freezing the crystal in liquid nitrogen, the mother liquor was supplemented with 10 mM CoA and 40 % (w/v) PEG200.

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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: 1.81→29.99 Å / Num. obs: 136868 / % possible obs: 99.8 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.024 / Rrim(I) all: 0.073 / Net I/σ(I): 18.4 / Num. measured all: 1245111
Reflection shellResolution: 1.81→1.91 Å / % possible obs: 99.2 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.908 / Num. measured all: 180122 / Num. unique obs: 19659 / CC1/2: 0.811 / Rpim(I) all: 0.313 / Rrim(I) all: 0.962 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20210323data reduction
SCALA3.3.22data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→29.99 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.91 / Phase error: 16.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 2008 1.47 %
Rwork0.1576 --
obs0.1579 136762 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9423 0 128 916 10467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079743
X-RAY DIFFRACTIONf_angle_d0.87613208
X-RAY DIFFRACTIONf_dihedral_angle_d20.2463502
X-RAY DIFFRACTIONf_chiral_restr0.0561439
X-RAY DIFFRACTIONf_plane_restr0.0081744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.27611380.25049371X-RAY DIFFRACTION98
1.86-1.910.2461460.21239540X-RAY DIFFRACTION100
1.91-1.960.23351380.18269543X-RAY DIFFRACTION100
1.96-2.020.2061410.17199560X-RAY DIFFRACTION100
2.02-2.10.21121390.16889542X-RAY DIFFRACTION100
2.1-2.180.19731480.15489539X-RAY DIFFRACTION100
2.18-2.280.17271470.15399599X-RAY DIFFRACTION100
2.28-2.40.19971410.16039606X-RAY DIFFRACTION100
2.4-2.550.17871410.15589602X-RAY DIFFRACTION100
2.55-2.750.16331360.16089626X-RAY DIFFRACTION100
2.75-3.020.17341490.16619635X-RAY DIFFRACTION100
3.02-3.460.21511460.16459715X-RAY DIFFRACTION100
3.46-4.360.14661480.13559783X-RAY DIFFRACTION100
4.36-29.990.15191500.148410093X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 81.1957 Å / Origin y: 1.1264 Å / Origin z: 31.0827 Å
111213212223313233
T0.1897 Å20.0207 Å2-0.0214 Å2-0.1882 Å20.0115 Å2--0.2025 Å2
L0.2693 °20.1219 °2-0.0501 °2-0.277 °20.0668 °2--0.41 °2
S-0.0133 Å °0.0175 Å °0.0115 Å °-0.0097 Å °0.0115 Å °0.0012 Å °-0.0051 Å °-0.0081 Å °0.0029 Å °
Refinement TLS groupSelection details: all

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