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- PDB-9rcp: 1,2-propanediol dehydratase with 0.1 % 1,3-propanediol additive -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9rcp
Title1,2-propanediol dehydratase with 0.1 % 1,3-propanediol 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: 1.9 Å
AuthorsKalnins, G. / Estere, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 1,2-propanediol dehydratase with 0.1 % 1,3-propanediol 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)366,5909
Polymers366,2804
Non-polymers3105
Water26,4461468
1
A: Glycyl radical protein
B: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,3265
Polymers183,1402
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-1 kcal/mol
Surface area49820 Å2
MethodPISA
2
C: Glycyl radical protein
D: 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 area2870 Å2
ΔGint-5 kcal/mol
Surface area50280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.435, 200.574, 118.108
Angle α, β, γ (deg.)90.000, 106.589, 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1468 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.6 M ammonium acetate, 3.6% 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: 1.9→100.29 Å / Num. obs: 284309 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.85 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.101 / Rrim(I) all: 0.193 / Χ2: 0.91 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7 % / Rmerge(I) obs: 1.592 / Mean I/σ(I) obs: 1 / Num. unique obs: 14032 / CC1/2: 0.491 / Rpim(I) all: 1.003 / Rrim(I) all: 1.886 / Χ2: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→75.06 Å / SU ML: 0.2494 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 14126 4.97 %
Rwork0.1859 270002 -
obs0.1878 284128 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→75.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25004 0 20 1468 26492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007425806
X-RAY DIFFRACTIONf_angle_d0.960635006
X-RAY DIFFRACTIONf_chiral_restr0.05343765
X-RAY DIFFRACTIONf_plane_restr0.00724662
X-RAY DIFFRACTIONf_dihedral_angle_d18.85693564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.34394340.31248992X-RAY DIFFRACTION99.95
1.92-1.940.32574890.29858995X-RAY DIFFRACTION99.89
1.94-1.970.30264820.28418926X-RAY DIFFRACTION99.9
1.97-1.990.34014820.28828973X-RAY DIFFRACTION99.9
1.99-2.020.3234630.27328953X-RAY DIFFRACTION99.93
2.02-2.050.29544760.26269049X-RAY DIFFRACTION99.96
2.05-2.080.27964900.25068920X-RAY DIFFRACTION99.96
2.08-2.110.2984760.25018953X-RAY DIFFRACTION99.93
2.11-2.140.27994710.24049013X-RAY DIFFRACTION99.95
2.14-2.170.27734120.23299035X-RAY DIFFRACTION99.96
2.17-2.210.28244840.23178969X-RAY DIFFRACTION99.96
2.21-2.250.28934790.22728946X-RAY DIFFRACTION99.97
2.25-2.30.2574370.22029046X-RAY DIFFRACTION100
2.3-2.340.27524450.2169002X-RAY DIFFRACTION99.93
2.34-2.390.25535040.20778975X-RAY DIFFRACTION99.96
2.39-2.450.26734280.20019032X-RAY DIFFRACTION99.99
2.45-2.510.27424730.20278972X-RAY DIFFRACTION99.99
2.51-2.580.24644530.19839024X-RAY DIFFRACTION99.99
2.58-2.650.24614680.1969006X-RAY DIFFRACTION100
2.65-2.740.24434820.18749022X-RAY DIFFRACTION99.99
2.74-2.840.23115080.18418934X-RAY DIFFRACTION99.99
2.84-2.950.24544130.19159076X-RAY DIFFRACTION100
2.95-3.090.23724610.18669001X-RAY DIFFRACTION100
3.09-3.250.20494730.18289032X-RAY DIFFRACTION99.99
3.25-3.450.23185130.18628935X-RAY DIFFRACTION100
3.45-3.720.20375050.17189045X-RAY DIFFRACTION100
3.72-4.090.17534950.15038998X-RAY DIFFRACTION100
4.09-4.690.16024730.13349004X-RAY DIFFRACTION99.99
4.69-5.90.16334960.13859054X-RAY DIFFRACTION99.99
5.9-75.060.14194610.12759120X-RAY DIFFRACTION99.68

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