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- PDB-1uc4: Structure of diol dehydratase complexed with (S)-1,2-propanediol -

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Basic information

Entry
Database: PDB / ID: 1uc4
TitleStructure of diol dehydratase complexed with (S)-1,2-propanediol
Components(diol dehydrase ...) x 3
KeywordsLYASE / ALPHA/BETA BARREL
Function / homology
Function and homology information


propanediol dehydratase / propanediol dehydratase activity / cobalamin binding / metal ion binding
Similarity search - Function
Propanediol/glycerol dehydratase, small subunit / Diol/glycerol dehydratase, large subunit / Hypothetical Protein Yqey; Chain: A; domain1 / 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 ...Propanediol/glycerol dehydratase, small subunit / Diol/glycerol dehydratase, large subunit / Hypothetical Protein Yqey; Chain: A; domain1 / 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 dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Cobalamin (vitamin B12)-dependent enzyme, catalytic / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYANOCOBALAMIN / : / 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: 1.8 Å
AuthorsShibata, N. / Nakanishi, Y. / Fukuoka, M. / Yamanishi, M. / Yasuoka, N. / Toraya, T.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase
Authors: Shibata, N. / Nakanishi, Y. / Fukuoka, M. / Yamanishi, M. / Yasuoka, N. / Toraya, T.
History
DepositionApr 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 25, 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
G: diol dehydrase gamma subunit
L: diol dehydrase alpha subunit
E: diol dehydrase beta subunit
M: diol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,51216
Polymers207,4976
Non-polymers3,01510
Water25,4191411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31150 Å2
ΔGint-126 kcal/mol
Surface area51540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.830, 121.950, 208.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein diol dehydrase alpha subunit / Diol dehydratase / alpha subunit


Mass: 60408.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59470, propanediol dehydratase
#2: Protein diol dehydrase beta subunit / Diol dehydratase / beta subunit


Mass: 24141.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59471, propanediol dehydratase
#3: Protein diol dehydrase gamma subunit / Diol dehydratase / gamma subunit


Mass: 19198.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59472, propanediol dehydratase

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Non-polymers , 5 types, 1421 molecules

#4: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-CNC / CYANOCOBALAMIN / Cyanocobalamin


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Comment: medication*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1411 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8
Details: PEG6000, ammonium sulfate, Tris, (S)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: sandwich-drop vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150-60 mg/mlprotein1drop
215 %(w/v)PEG60001reservoir
30.23 Mammonium sulfate1reservoir
40.02 MTris-HCl1reservoirpH8.0
50.2 %LDAO1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.119 / % possible all: 0.671
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 152278 / Num. measured all: 1991323
Reflection shell
*PLUS
% possible obs: 67.1 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EGM

1egm


Resolution: 1.8→36.92 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 14391 RANDOM
Rwork0.195 --
obs0.195 174276 -
all-174276 -
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13295 0 198 1411 14904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.8-1.910.295522080.2667X-RAY DIFFRACTION204896
1.91-2.060.264724760.2359X-RAY DIFFRACTION215616
2.06-2.270.241824090.203X-RAY DIFFRACTION221056
2.27-2.590.230824690.1904X-RAY DIFFRACTION221876
2.59-3.270.234723860.1868X-RAY DIFFRACTION224466
3.27-36.920.205824430.1779X-RAY DIFFRACTION211366
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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