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- PDB-9fd7: Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphat... -

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Basic information

Entry
Database: PDB / ID: 9fd7
TitleRe-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase in substrate-free state
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,8927
Polymers57,4312
Non-polymers4605
Water3,729207
1
A: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8082
Polymers28,7161
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0845
Polymers28,7161
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.173, 72.752, 70.919
Angle α, β, γ (deg.)90.00, 96.19, 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, S239GEs
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 42.82 %
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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.4→72.75 Å / Num. obs: 91423 / % possible obs: 95.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Χ2: 0.97 / Net I/σ(I): 16.9 / Num. measured all: 604885
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 76.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.796 / Num. measured all: 20006 / Num. unique obs: 3626 / CC1/2: 0.746 / Rpim(I) all: 0.354 / Rrim(I) all: 0.875 / Χ2: 0.98 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→50.68 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.967 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15708 4462 4.9 %RANDOM
Rwork0.13386 ---
obs0.13502 86934 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-1.22 Å2
2---1.35 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.4→50.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 30 207 3888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123780
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163754
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.7865112
X-RAY DIFFRACTIONr_angle_other_deg0.5911.7278652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.659524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33410670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0194395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.018785
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_it3.8391.4951971
X-RAY DIFFRACTIONr_mcbond_other3.8231.4951971
X-RAY DIFFRACTIONr_mcangle_it5.42.6862465
X-RAY DIFFRACTIONr_mcangle_other5.4032.6872466
X-RAY DIFFRACTIONr_scbond_it6.6421.8431809
X-RAY DIFFRACTIONr_scbond_other6.6411.8441810
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4993.2182642
X-RAY DIFFRACTIONr_long_range_B_refined11.89715.844253
X-RAY DIFFRACTIONr_long_range_B_other11.89915.844254
X-RAY DIFFRACTIONr_rigid_bond_restr4.11837534
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 284 -
Rwork0.239 5345 -
obs--79.89 %

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