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

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Basic information

Entry
Database: PDB / ID: 9rcr
Title1,2-propanediol dehydratase with 0.1 % 1,2-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
R-1,2-PROPANEDIOL / Glycyl radical protein
Similarity search - Component
Biological speciesRaoultella planticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKalnins, G. / Estere, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 1,2-propanediol dehydratase with 0.1 % 1,2-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)366,5848
Polymers366,2804
Non-polymers3044
Water2,270126
1
A: Glycyl radical protein
B: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2924
Polymers183,1402
Non-polymers1522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-6 kcal/mol
Surface area49700 Å2
MethodPISA
2
C: Glycyl radical protein
D: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2924
Polymers183,1402
Non-polymers1522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-6 kcal/mol
Surface area50050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.890, 199.973, 118.377
Angle α, β, γ (deg.)90.000, 106.323, 90.000
Int Tables number4
Space group name H-MP1211
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-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 50.97 %
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: 2.8→98.78 Å / Num. obs: 86164 / % possible obs: 97.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.67 Å2 / CC1/2: 0.3 / Rmerge(I) obs: 0.858 / Rpim(I) all: 0.561 / Rrim(I) all: 1.03 / Χ2: 0.97 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 5.835 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4143 / CC1/2: 0.192 / Rpim(I) all: 4.087 / Rrim(I) all: 11.338 / Χ2: 1.03 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→98.7 Å / Cor.coef. Fo:Fc: 0.81 / Cor.coef. Fo:Fc free: 0.75 / SU B: 32.264 / SU ML: 0.544 / Cross valid method: FREE R-VALUE / ESU R Free: 0.506
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3178 4009 4.664 %
Rwork0.2626 81956 -
all0.265 --
obs-85965 97.074 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.739 Å2
Baniso -1Baniso -2Baniso -3
1-1.912 Å20 Å21.34 Å2
2---2.38 Å2-0 Å2
3----0.271 Å2
Refinement stepCycle: LAST / Resolution: 2.8→98.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25001 0 15 126 25142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01325575
X-RAY DIFFRACTIONr_bond_other_d0.0090.01523753
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.64534642
X-RAY DIFFRACTIONr_angle_other_deg1.511.5854590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57853168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62322.3631477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81154229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.09915184
X-RAY DIFFRACTIONr_chiral_restr0.0720.23278
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0229637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026215
X-RAY DIFFRACTIONr_nbd_refined0.2040.26298
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.225344
X-RAY DIFFRACTIONr_nbtor_refined0.1750.212939
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.212588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2730
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0940.235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2820.210
X-RAY DIFFRACTIONr_nbd_other0.3250.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.330.26
X-RAY DIFFRACTIONr_mcbond_it1.5712.85112678
X-RAY DIFFRACTIONr_mcbond_other1.572.8512677
X-RAY DIFFRACTIONr_mcangle_it2.4384.27215841
X-RAY DIFFRACTIONr_mcangle_other2.4384.27215842
X-RAY DIFFRACTIONr_scbond_it1.8862.92312897
X-RAY DIFFRACTIONr_scbond_other1.8862.92312898
X-RAY DIFFRACTIONr_scangle_it2.7794.34318800
X-RAY DIFFRACTIONr_scangle_other2.7794.34318801
X-RAY DIFFRACTIONr_lrange_it3.64233.53429524
X-RAY DIFFRACTIONr_lrange_other3.64233.53429525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.5052850.4795763X-RAY DIFFRACTION92.4629
2.873-2.9510.4842900.4415620X-RAY DIFFRACTION93.5275
2.951-3.0370.442740.3975589X-RAY DIFFRACTION94.4579
3.037-3.130.4082740.3715451X-RAY DIFFRACTION94.9735
3.13-3.2330.3642280.3365344X-RAY DIFFRACTION95.7388
3.233-3.3460.382160.3175208X-RAY DIFFRACTION96.3068
3.346-3.4720.3332640.2855027X-RAY DIFFRACTION97.3147
3.472-3.6140.2972260.2484894X-RAY DIFFRACTION97.5238
3.614-3.7750.2852370.2164692X-RAY DIFFRACTION98.1091
3.775-3.9590.2892110.1984543X-RAY DIFFRACTION98.8769
3.959-4.1720.2572450.1814273X-RAY DIFFRACTION98.9488
4.172-4.4250.2231980.1614105X-RAY DIFFRACTION98.7833
4.425-4.730.2571860.1633880X-RAY DIFFRACTION99.5349
4.73-5.1080.2611850.1723567X-RAY DIFFRACTION99.6018
5.108-5.5950.2481510.1893338X-RAY DIFFRACTION99.8283
5.595-6.2530.2531540.2053016X-RAY DIFFRACTION99.6855
6.253-7.2170.2371280.192649X-RAY DIFFRACTION99.8921
7.217-8.830.2361130.1782257X-RAY DIFFRACTION99.8736
8.83-12.450.23920.1891752X-RAY DIFFRACTION100
12.45-98.70.268520.306988X-RAY DIFFRACTION99.7124

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