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- PDB-9fd9: Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphat... -

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Basic information

Entry
Database: PDB / ID: 9fd9
TitleRe-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase, Schiff-base complex with 4-nitro-cinnamaldehyde
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE / protein engineering / directed evolution / aldolase / peroxygenase / Schiff base
Function / homology
Function and homology information


deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / 2-deoxyribose 1-phosphate catabolic process / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm
Similarity search - Function
Deoxyribose-phosphate aldolase type II / Deoxyribose-phosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å
AuthorsThunnissen, A.M.W.H. / Zhou, H. / Frietema, H.O.T. / Poelarends, G.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)724.016.002 Netherlands
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Engineering 2-Deoxy-D-ribose-5-phosphate Aldolase for anti- and syn-Selective Epoxidations of alpha , beta-Unsaturated Aldehydes.
Authors: Zhou, H. / Kunzendorf, A. / Xu, G. / Frietema, H.O.T. / Thunnissen, A.W.H. / Poelarends, G.J.
History
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyribose-phosphate aldolase
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8825
Polymers57,4312
Non-polymers4503
Water4,432246
1
A: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9873
Polymers28,7161
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8952
Polymers28,7161
Non-polymers1791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.095, 72.531, 70.688
Angle α, β, γ (deg.)90.00, 96.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deoxyribose-phosphate aldolase / DERA / 2-deoxy-D-ribose 5-phosphate aldolase / Phosphodeoxyriboaldolase / Deoxyriboaldolase


Mass: 28715.734 Da / Num. of mol.: 2
Mutation: T18S, L20S, D22G, D24Y, C47S, I48V, F52S, K172R, T197S, P202V, A203T, R207S, G236S, S239G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: deoC, EcolC_3675 / Production host: Escherichia coli (E. coli) / References: UniProt: B1IS38, deoxyribose-phosphate aldolase
#2: Chemical ChemComp-A1IB9 / 4-nitro-cinnamaldehyde / (~{E})-3-(4-nitrophenyl)prop-2-en-1-ol


Mass: 179.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Protein was concentrated to 8 mg/mL in 20 mM potassium phosphate, pH 7. Crystallization conditions: 0-4% 2-propanol, 22-24% PEG 3350 in 0.1 M HEPES, pH 7.5. The Schiff-base complex was ...Details: Protein was concentrated to 8 mg/mL in 20 mM potassium phosphate, pH 7. Crystallization conditions: 0-4% 2-propanol, 22-24% PEG 3350 in 0.1 M HEPES, pH 7.5. The Schiff-base complex was obtained by brief soaking (about 30 seconds) in saturated ligand solution prepared with crystallization solution plus 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.52→47.81 Å / Num. obs: 70796 / % possible obs: 95.5 % / Redundancy: 2.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.072 / Rrim(I) all: 0.115 / Χ2: 1.07 / Net I/σ(I): 7 / Num. measured all: 164586
Reflection shellResolution: 1.52→1.55 Å / % possible obs: 93.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 1.155 / Num. measured all: 8355 / Num. unique obs: 3451 / CC1/2: 0.312 / Rpim(I) all: 0.9 / Rrim(I) all: 1.471 / Χ2: 1.04 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.52→41.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.87 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21755 3406 4.8 %RANDOM
Rwork0.18633 ---
obs0.18777 67356 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å20.04 Å2
2--0.69 Å20 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.52→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 30 246 3918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123802
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163770
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.7865149
X-RAY DIFFRACTIONr_angle_other_deg0.5971.7278683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.5325.96831
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21410680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0194469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.018803
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3621.41982
X-RAY DIFFRACTIONr_mcbond_other1.3311.3991982
X-RAY DIFFRACTIONr_mcangle_it1.9912.4962484
X-RAY DIFFRACTIONr_mcangle_other1.9912.4972485
X-RAY DIFFRACTIONr_scbond_it2.6051.7181820
X-RAY DIFFRACTIONr_scbond_other2.6051.7181821
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0682.9972660
X-RAY DIFFRACTIONr_long_range_B_refined5.2715.124407
X-RAY DIFFRACTIONr_long_range_B_other5.21214.524359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 259 -
Rwork0.334 4930 -
obs--94.05 %
Refinement TLS params.

T33: 0.0044 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42650.044-0.10530.16040.18940.28640.0113-0.0010.02430.0055-0.0012-0.00070.00690.0131-0.01010.02040.00480.00360.08440.00334.5746-8.02050.2682
20.6457-0.0843-0.11130.02550.11120.66910.01210.04550.04880.0059-0.0082-0.00560.0414-0.0337-0.00390.0133-0.00420.00350.092-0.0013-1.0033-21.3769-35.7459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 302
2X-RAY DIFFRACTION2B3 - 301

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