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- PDB-9hnf: Beta-keto acid cleavage enzyme from Paracoccus denitrificans with... -

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Basic information

Entry
Database: PDB / ID: 9hnf
TitleBeta-keto acid cleavage enzyme from Paracoccus denitrificans with bound acetoacetate and acetyl-CoA
Components3-keto-5-aminohexanoate cleavage protein
KeywordsLYASE / aldolase / acetyl-CoA / acetoacetate / 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 / ACETOACETIC ACID / ACETYL COENZYME *A / 3-keto-5-aminohexanoate cleavage protein
Function and homology information
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)74,8108
Polymers72,8562
Non-polymers1,9546
Water4,558253
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)149,62116
Polymers145,7134
Non-polymers3,90812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area16470 Å2
ΔGint-168 kcal/mol
Surface area38640 Å2
Unit cell
Length a, b, c (Å)80.900, 138.480, 136.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 36428.133 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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AAE / ACETOACETIC ACID


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.8
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 10 % (v/v) pentaerythritol ethoxylate, 10 % v/v 1-Butanol. The final ...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 10 % (v/v) pentaerythritol ethoxylate, 10 % v/v 1-Butanol. The final size of the drops was 1 microliter. Prior to flash freezing the crystals in liquid nitrogen, the mother liquor was supplemented with 15 mM acetyl-CoA, 20 mM acetoacetate, and 20 % (v/v) pentaerythrol propoxylate.

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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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→27.69 Å / Num. obs: 44681 / % possible obs: 99.4 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.032 / Rrim(I) all: 0.119 / Χ2: 0.99 / Net I/σ(I): 14.4 / Num. measured all: 591673
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3628 / CC1/2: 0.884 / Rpim(I) all: 0.234 / Rrim(I) all: 0.874 / Χ2: 0.78 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimless0.7.9data scaling
XDS20240723data reduction
PHASER1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.69 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 1993 4.46 %
Rwork0.1752 --
obs0.1759 44675 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 118 253 5069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034914
X-RAY DIFFRACTIONf_angle_d0.626670
X-RAY DIFFRACTIONf_dihedral_angle_d13.0881808
X-RAY DIFFRACTIONf_chiral_restr0.043731
X-RAY DIFFRACTIONf_plane_restr0.005875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.29341410.24742994X-RAY DIFFRACTION99
2.15-2.210.27851380.24763013X-RAY DIFFRACTION100
2.21-2.280.38321400.34072922X-RAY DIFFRACTION96
2.28-2.350.23751370.21733057X-RAY DIFFRACTION100
2.35-2.430.25531420.19413052X-RAY DIFFRACTION100
2.43-2.530.21761480.18513020X-RAY DIFFRACTION100
2.53-2.650.21681450.1913021X-RAY DIFFRACTION100
2.65-2.780.24591370.19343058X-RAY DIFFRACTION99
2.78-2.960.2221380.19613024X-RAY DIFFRACTION99
2.96-3.190.20461470.1923045X-RAY DIFFRACTION100
3.19-3.510.22831420.1723086X-RAY DIFFRACTION100
3.51-4.010.16691450.15193066X-RAY DIFFRACTION100
4.01-5.050.12581450.13373111X-RAY DIFFRACTION100
5.05-27.690.14431480.14813213X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.0053 Å / Origin y: -13.2895 Å / Origin z: 10.7673 Å
111213212223313233
T0.2903 Å2-0.0015 Å2-0.0019 Å2-0.2568 Å2-0.0118 Å2--0.254 Å2
L1.1616 °2-0.1417 °2-0.0861 °2-0.6134 °2-0.2203 °2--0.5632 °2
S-0.048 Å °-0.1467 Å °-0.0707 Å °0.0004 Å °0.0453 Å °-0.0159 Å °0.0701 Å °0.0259 Å °0.0021 Å °
Refinement TLS groupSelection details: all

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