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- PDB-7xrl: Diol dehydratase complexed with AdoMeCbl and 1,2-propanediol -

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Basic information

Entry
Database: PDB / ID: 7xrl
TitleDiol dehydratase complexed with AdoMeCbl and 1,2-propanediol
Components(Diol dehydrase ...) x 3
KeywordsLYASE / Adenosylcobalamin / Radical enzyme
Function / homology
Function and homology information


propanediol dehydratase / propanediol dehydratase activity / cobalamin binding / metal ion binding
Similarity search - Function
Diol/glycerol dehydratase, large subunit / Propanediol/glycerol dehydratase, small subunit / Propanediol/glycerol dehydratase, medium subunit / Propanediol/glycerol dehydratase, small subunit superfamily / Diol/glycerol dehydratase, large subunit superfamily / Dehydratase large subunit / Dehydratase small subunit / Diol/glycerol dehydratase/dehydratase reactivating factor / Dehydratase medium subunit / B12-dependent dehydratases, beta subunit / Cobalamin (vitamin B12)-dependent enzyme, catalytic
Similarity search - Domain/homology
COBALAMIN / Chem-FWK / : / AMMONIUM ION / S-1,2-PROPANEDIOL / Diol dehydrase alpha subunit / Diol dehydrase beta subunit / Diol dehydrase gamma subunit
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsShibata, N. / Toraya, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemistry / Year: 2022
Title: Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Authors: Shibata, N. / Higuchi, Y. / Krautler, B. / Toraya, T.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diol dehydrase alpha subunit
B: Diol dehydrase beta subunit
C: Diol dehydrase gamma subunit
D: Diol dehydrase alpha subunit
E: Diol dehydrase beta subunit
F: Diol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,02118
Polymers195,4846
Non-polymers3,53812
Water28,2661569
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27100 Å2
ΔGint-136 kcal/mol
Surface area54330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.718, 117.246, 201.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Diol dehydrase ... , 3 types, 6 molecules ADBECF

#1: Protein Diol dehydrase alpha subunit / Propanediol dehydratase / Propanediol dehydratase large subunit


Mass: 60408.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: pddA, pduC, AB185_12495, SAMEA2273575_05741 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q59470, propanediol dehydratase
#2: Protein Diol dehydrase beta subunit


Mass: 21721.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: pddB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q59471, propanediol dehydratase
#3: Protein Diol dehydrase gamma subunit / Propanediol dehydratase / Propanediol dehydratase small subunit


Mass: 15611.735 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria)
Gene: pddC, pduE, pduE_1, AB185_12485, SAMEA2273639_01293, SAMEA2273697_01477
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q59472, propanediol dehydratase

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Non-polymers , 7 types, 1581 molecules

#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#8: Chemical ChemComp-FWK / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol


Mass: 265.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1569 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% (w/v) PEG6000, 50 mM HEPES pH 8.0, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→46 Å / Num. obs: 176732 / % possible obs: 99.9 % / Redundancy: 5.97 % / Biso Wilson estimate: 15.28 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.141 / Net I/σ(I): 15.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 8717 / CC1/2: 0.498 / Rrim(I) all: 0.782 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IWB

1iwb


Resolution: 1.75→45.72 Å / SU ML: 0.2107 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.4313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2056 4910 2.78 %
Rwork0.167 171705 -
obs0.1681 176615 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.47 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13335 0 236 1569 15140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006213883
X-RAY DIFFRACTIONf_angle_d1.036118898
X-RAY DIFFRACTIONf_chiral_restr0.05222137
X-RAY DIFFRACTIONf_plane_restr0.00782487
X-RAY DIFFRACTIONf_dihedral_angle_d14.57895289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.33871600.30445587X-RAY DIFFRACTION99.15
1.77-1.790.32981620.29335673X-RAY DIFFRACTION99.74
1.79-1.810.32611620.2935645X-RAY DIFFRACTION99.83
1.81-1.830.28981630.27525695X-RAY DIFFRACTION99.93
1.83-1.860.34211610.26795628X-RAY DIFFRACTION99.86
1.86-1.880.29531630.25755715X-RAY DIFFRACTION99.86
1.88-1.910.31271620.24395626X-RAY DIFFRACTION99.86
1.91-1.940.27041630.23175706X-RAY DIFFRACTION99.91
1.94-1.970.27951620.22175677X-RAY DIFFRACTION99.9
1.97-20.24751620.21455684X-RAY DIFFRACTION99.91
2-2.040.25971620.20055672X-RAY DIFFRACTION99.91
2.04-2.070.23981620.1885662X-RAY DIFFRACTION99.91
2.07-2.110.22411630.18035710X-RAY DIFFRACTION99.97
2.11-2.160.23481620.16175682X-RAY DIFFRACTION99.93
2.16-2.20.19041650.15695702X-RAY DIFFRACTION99.83
2.2-2.250.22111610.15795693X-RAY DIFFRACTION99.93
2.25-2.310.18951650.15425725X-RAY DIFFRACTION99.92
2.31-2.370.20161560.15035684X-RAY DIFFRACTION99.88
2.37-2.440.19461750.1515718X-RAY DIFFRACTION100
2.44-2.520.20281560.1495723X-RAY DIFFRACTION99.9
2.52-2.610.19551560.14385720X-RAY DIFFRACTION99.86
2.61-2.720.18921760.1445746X-RAY DIFFRACTION99.97
2.72-2.840.17351700.1475733X-RAY DIFFRACTION99.95
2.84-2.990.19071550.14925730X-RAY DIFFRACTION99.97
2.99-3.180.19791620.15315773X-RAY DIFFRACTION99.97
3.18-3.420.17961730.14865769X-RAY DIFFRACTION99.98
3.42-3.760.15621640.13265808X-RAY DIFFRACTION99.93
3.76-4.310.13561650.12225843X-RAY DIFFRACTION100
4.31-5.430.16831700.1325868X-RAY DIFFRACTION99.98
5.43-45.720.19071720.15596108X-RAY DIFFRACTION99.6
Refinement TLS params.

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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2588580123910.001711022907480.01993017116290.2690744981870.09012502481710.412307837378-0.0165074920304-0.01567056368540.0113304883602-0.00319871223-0.002964381564290.0111160535433-0.0230263535407-0.0003678057769730.01857821485860.0655092554382-0.00626432753924-0.007310006039650.05980836107650.004452572272310.08984307222210.264447236-3.9779327645336.4092441494
21.514515521750.168458673230.1253482355411.071993910110.2712787597911.12784099367-0.107939705253-0.1086651134530.2546991459260.007865029409090.059487652105-0.0137287802365-0.01549954853610.04930309392710.02355151633280.12983346599-0.0200926802403-0.01551328533450.148666072131-0.01846388506860.18806469676527.309965182814.016556900444.6145360749
31.11488355295-0.1139142049440.03348106480830.472291046733-0.0007165062467080.589660513156-0.0120515580915-0.202486897182-0.07750225563010.1470918365540.007841387380090.0425951633131-0.0114268670985-0.02520856108960.0025629340980.179124651665-0.01268730112790.003027681148310.1491407931530.03409460450780.1315636791591.25270617381-15.987383685357.5872956741
40.4382449023620.1661575230820.4143339212740.4063437775670.3013658043011.32731212299-0.09204627788710.210073048320.0304746721631-0.1399032412880.05383303794550.000676359595054-0.2012108775140.1870162271860.01135751599980.139194420553-0.039484699344-0.01220451084360.1379592633420.02971720937680.103451849333-0.644081102224-2.69558489619-2.83003511344
50.9046157555870.0153411928199-0.06863333161620.894884687863-0.4491266222921.0213383301-0.1978188936130.3663520587920.385955811854-0.5589579147650.1599339832280.290735287412-1.27844698591-0.662234235421-0.1067149646241.298270730390.356178339212-0.2422016629860.505980743870.1184375186250.384223113984-25.49215034418.0570431681-10.2689540342
61.043603636330.06413892798210.1155037507090.5636299893930.1252542943231.19965545763-0.06025443853920.420707759496-0.0650166281307-0.14086713190.0863700342356-0.0585091519074-0.08182884405780.2217721841880.04535349923940.192676648807-0.03929726085570.007853616470370.324421404967-0.03110629087630.120888561532-2.77991604357-13.2943034954-24.8278769446
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 552)AA - B1 - 5521
22(chain 'B' and resid 46 through 224)BF - G46 - 2241
33(chain 'C' and resid 38 through 173)CH38 - 1731 - 136
44(chain 'D' and resid 1 through 554)DI - J1 - 5541
55(chain 'E' and resid 46 through 223)EN - O46 - 2231
66(chain 'F' and resid 38 through 173)FP38 - 1731 - 136

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