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- PDB-1dio: DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA -

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Basic information

Entry
Database: PDB / ID: 1dio
TitleDIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
Components(PROTEIN (DIOL ...) x 3
KeywordsLYASE / COENZYME B12 / PROPANEDIOL / POTASSIUM ION / TIM 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
COBALAMIN / : / 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 / MIR / Resolution: 2.2 Å
AuthorsShibata, N. / Masuda, J. / Tobimatsu, T. / Toraya, T. / Suto, K. / Morimoto, Y. / Yasuoka, N.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Authors: Shibata, N. / Masuda, J. / Tobimatsu, T. / Toraya, T. / Suto, K. / Morimoto, Y. / Yasuoka, N.
History
DepositionJan 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 30, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (DIOL DEHYDRATASE)
B: PROTEIN (DIOL DEHYDRATASE)
G: PROTEIN (DIOL DEHYDRATASE)
L: PROTEIN (DIOL DEHYDRATASE)
E: PROTEIN (DIOL DEHYDRATASE)
M: PROTEIN (DIOL DEHYDRATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,38812
Polymers207,4976
Non-polymers2,8916
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26210 Å2
ΔGint-132 kcal/mol
Surface area52780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.200, 122.300, 209.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.97183, -0.23498, -0.01809), (-0.2349, 0.95962, 0.15477), (-0.01901, 0.15466, -0.98779)160.06094, -10.86044, 380.73428
2given(-0.96957, -0.24294, -0.0302), (-0.24467, 0.95739, 0.15342), (-0.00836, 0.15614, -0.9877)161.98659, -9.81904, 379.76443
3given(-0.96938, -0.24358, -0.03124), (-0.24549, 0.95784, 0.14924), (-0.00643, 0.15234, -0.98831)162.42407, -8.96189, 379.74799

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Components

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PROTEIN (DIOL ... , 3 types, 6 molecules ALBEGM

#1: Protein PROTEIN (DIOL DEHYDRATASE)


Mass: 60408.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Description: SYNTHETIC GENE; / Plasmid: PUC119 / Culture collection (production host): ATCC 8724 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q59470, propanediol dehydratase
#2: Protein PROTEIN (DIOL DEHYDRATASE)


Mass: 24141.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Description: SYNTHETIC GENE; / Plasmid: PUC119 / Culture collection (production host): ATCC 8724 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q59471, propanediol dehydratase
#3: Protein PROTEIN (DIOL DEHYDRATASE)


Mass: 19198.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Description: SYNTHETIC GENE / Plasmid: PUC119 / Culture collection (production host): ATCC 8724 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q59472, propanediol dehydratase

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Non-polymers , 4 types, 402 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE IS DESCRIBED IN TOBIMATSU ET AL.(1995) J.BIOL.

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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: 2.3 Å3/Da / Density % sol: 44 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD.
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: sandwich-drop vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG60001reservoir
20.24 Mammonium sulfate1reservoir
320 mMTris-HCl1reservoir
40.20 %LDAO1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708
DetectorDetector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 86302 / % possible obs: 83.5 % / Redundancy: 2.95 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.51
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 2.32 / % possible all: 64.5
Reflection
*PLUS
Num. measured all: 384295
Reflection shell
*PLUS
% possible obs: 64.5 %

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→10 Å / SU B: 7.38 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4232 5 %RANDOM
Rwork0.187 ---
obs0.188 84269 83.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13322 0 194 396 13912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 85400
Solvent computation
*PLUS
Displacement parameters
*PLUS

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