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- PDB-9rco: 1,2-propanediol dehydratase with 0.1 % glycerol additive -

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Basic information

Entry
Database: PDB / ID: 9rco
Title1,2-propanediol dehydratase with 0.1 % glycerol additive
ComponentsGlycyl radical protein
KeywordsLYASE / glycyl radical enzyme / 1 / 2-propanediol
Function / homology
Function and homology information


lyase activity / cytosol
Similarity search - Function
: / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
Glycyl radical protein
Similarity search - Component
Biological speciesRaoultella planticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKalnins, G. / Estere, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 1,2-propanediol dehydratase with 0.1 % glycerol additive
Authors: Kalnins, G. / Estere, M.
History
DepositionMay 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycyl radical protein
B: Glycyl radical protein
C: Glycyl radical protein
D: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,71210
Polymers366,2804
Non-polymers4326
Water38,8222155
1
A: Glycyl radical protein
B: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2644
Polymers183,1402
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-4 kcal/mol
Surface area49870 Å2
MethodPISA
2
C: Glycyl radical protein
D: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,4486
Polymers183,1402
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-4 kcal/mol
Surface area49790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.529, 199.413, 118.100
Angle α, β, γ (deg.)90.000, 107.023, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Glycyl radical protein


Mass: 91569.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella planticola (bacteria) / Gene: I8Y23_000693 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAN5KVK2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2155 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.6 M ammonium acetate, 4% PEG 4000, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.7→99.71 Å / Num. obs: 387685 / % possible obs: 98.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.09 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.099 / Rrim(I) all: 0.189 / Χ2: 0.93 / Net I/σ(I): 7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.605 / Mean I/σ(I) obs: 1 / Num. unique obs: 18961 / CC1/2: 0.433 / Rpim(I) all: 0.98 / Rrim(I) all: 1.883 / Χ2: 0.88 / % possible all: 97.4

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Processing

Software
NameVersionClassification
xia2data reduction
PHENIX1.17.1_3660refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→72.61 Å / SU ML: 0.2116 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 19406 5.01 %
Rwork0.1816 367778 -
obs0.1831 387184 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→72.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25000 0 28 2155 27183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006725799
X-RAY DIFFRACTIONf_angle_d0.979434993
X-RAY DIFFRACTIONf_chiral_restr0.05323764
X-RAY DIFFRACTIONf_plane_restr0.00754659
X-RAY DIFFRACTIONf_dihedral_angle_d15.3743563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.33976640.306212018X-RAY DIFFRACTION97.26
1.72-1.740.34126470.301712084X-RAY DIFFRACTION96.72
1.74-1.760.31676490.284912067X-RAY DIFFRACTION97.36
1.76-1.780.29246150.27412109X-RAY DIFFRACTION97.14
1.78-1.810.29236210.266912132X-RAY DIFFRACTION97.14
1.81-1.830.28436350.259312080X-RAY DIFFRACTION97.49
1.83-1.860.29766440.267812227X-RAY DIFFRACTION97.4
1.86-1.890.29346760.26312046X-RAY DIFFRACTION97.59
1.89-1.910.27476340.250212163X-RAY DIFFRACTION97.75
1.91-1.950.26166380.233112200X-RAY DIFFRACTION97.54
1.95-1.980.25886300.227712192X-RAY DIFFRACTION97.84
1.98-2.020.26416180.227312225X-RAY DIFFRACTION98.17
2.02-2.050.24996320.212212227X-RAY DIFFRACTION98.03
2.05-2.10.25066340.206112167X-RAY DIFFRACTION97.82
2.1-2.140.24676270.199812281X-RAY DIFFRACTION98.11
2.14-2.190.23556720.198312268X-RAY DIFFRACTION98.49
2.19-2.250.23766360.195512225X-RAY DIFFRACTION98.59
2.25-2.310.2246320.191712317X-RAY DIFFRACTION98.63
2.31-2.380.22097020.18612230X-RAY DIFFRACTION98.65
2.38-2.450.20496500.173712326X-RAY DIFFRACTION98.68
2.45-2.540.20726340.177812288X-RAY DIFFRACTION98.6
2.54-2.640.21556700.176112320X-RAY DIFFRACTION98.89
2.64-2.760.21316480.168812390X-RAY DIFFRACTION99.26
2.76-2.910.20346010.171612436X-RAY DIFFRACTION99.04
2.91-3.090.20866680.169212358X-RAY DIFFRACTION99.43
3.09-3.330.19346920.167212365X-RAY DIFFRACTION99.32
3.33-3.660.18666990.160912420X-RAY DIFFRACTION99.57
3.66-4.190.16256700.138712433X-RAY DIFFRACTION99.6
4.19-5.280.15276280.133212552X-RAY DIFFRACTION99.75
5.28-72.610.15936400.147912632X-RAY DIFFRACTION99.74

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