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- PDB-7xrk: Diol dehydratase complexed with AdoMeCbl -

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Basic information

Entry
Database: PDB / ID: 7xrk
TitleDiol dehydratase complexed with AdoMeCbl
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 / : / 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: 2.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)198,83714
Polymers195,4876
Non-polymers3,3508
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28420 Å2
ΔGint-157 kcal/mol
Surface area53250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.313, 111.564, 197.058
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: 60410.062 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 , 5 types, 416 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: 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
#7: Chemical ChemComp-B12 / COBALAMIN


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


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.23 %
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 MX225HE / Detector: CCD / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→46 Å / Num. obs: 71587 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 21.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.143 / Net I/σ(I): 16.33
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 3279 / CC1/2: 0.839 / Rrim(I) all: 0.556 / % possible all: 91.9

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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: 2.3→45.07 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 1990 2.79 %
Rwork0.1651 69454 -
obs0.1667 71444 99.38 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13310 0 224 408 13942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004213776
X-RAY DIFFRACTIONf_angle_d0.948518736
X-RAY DIFFRACTIONf_chiral_restr0.04652114
X-RAY DIFFRACTIONf_plane_restr0.00552466
X-RAY DIFFRACTIONf_dihedral_angle_d10.16712007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.27721330.21194560X-RAY DIFFRACTION92.75
2.35-2.420.25571420.19424943X-RAY DIFFRACTION99.67
2.42-2.490.2711400.18234915X-RAY DIFFRACTION99.84
2.49-2.570.27771420.17364915X-RAY DIFFRACTION99.94
2.57-2.660.22291410.17414943X-RAY DIFFRACTION99.88
2.66-2.770.26391410.17164948X-RAY DIFFRACTION99.96
2.77-2.890.26411420.16844937X-RAY DIFFRACTION99.84
2.89-3.050.23421420.15974949X-RAY DIFFRACTION99.94
3.05-3.240.21721420.15674966X-RAY DIFFRACTION99.96
3.24-3.490.18711430.1554996X-RAY DIFFRACTION99.92
3.49-3.840.18211420.14175000X-RAY DIFFRACTION99.92
3.84-4.390.19551420.14065011X-RAY DIFFRACTION99.94
4.39-5.530.2121470.16125106X-RAY DIFFRACTION99.89
5.54-45.070.241510.18795265X-RAY DIFFRACTION99.74
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)
10.213319680660.02280216686290.01055356697220.34345361071-0.08099695220320.697400795813-0.003603929513250.04057506063430.0234799812827-0.01924592913830.01240260715370.00127397276013-0.02195942316580.00693895454505-0.008404647208180.0827514142932-0.00293937581127-0.003520569777420.09980815759690.001586587391680.10368959465935.1113061048-2.27738281678-35.078678567
21.09964548801-0.1512499738590.02665176487851.07379729338-0.09313868228021.10461236051-0.09420037185270.05609216170380.104683527778-0.06048693527450.03057857630220.1312231178240.001491014351050.01665702841580.05923911663540.156451192149-0.0246616725321-0.01629438287310.1567762811450.02493862085360.2508169025048.7622356711116.0868102315-42.6156163961
31.193765230510.109895729008-0.1706956944530.7376127269610.06046078226931.08567660782-0.03076954159810.235922477421-0.0182286799789-0.1848156739750.0487086992198-0.0433019884101-0.00460568949317-0.0869375390288-0.006536051255030.17256097580.00544966629638-0.004682572454220.1509172697870.00366401686520.13167849513933.4852999938-13.4816027426-56.7603680034
40.397092275-0.05372599684210.1715903634570.517419475436-0.1481346192711.04767297246-0.0547631430256-0.1232367508620.02172224302590.1295507806080.07248082649830.0293718857019-0.0816139488215-0.120956320801-0.01262307107680.1488108939460.01911228348-0.006346512783680.1448704806820.004447652554210.13677185681236.695876692-2.790303061254.17854339914
50.9607227761320.259761407644-0.1731292996931.094454767020.3978458754741.39032942276-0.100311401213-0.02157311260960.14640402201-0.06583995666380.122495261074-0.040369821112-0.2795127881520.304808667338-0.01289175129690.342531299293-0.068643340687-0.01961412708110.3167778395230.01180545143470.20034567773461.812759143916.942435879512.6935627061
60.980720424578-0.0125952722630.229141864531.00998333413-0.1476273347381.3349775422-0.0236010597949-0.342764116675-0.002887125585410.2328603579190.110134251170.1256191114660.0938030107637-0.272569010597-0.05777645169480.247257805180.000477315902019-0.006057476003540.3066494250630.05513325284090.16445569678138.5950760295-14.473627551625.7330846703
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A'AA - C2 - 16031
22chain 'B'BD - E46 - 16011
33chain 'C'CF38 - 1731 - 136
44chain 'D'DG - I1 - 16031
55chain 'E'EJ - K46 - 16011
66chain 'F'FL38 - 1721 - 135

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