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- PDB-1iwb: Crystal structure of diol dehydratase -

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Basic information

Entry
Database: PDB / ID: 1iwb
TitleCrystal structure of diol dehydratase
Components(DIOL DEHYDRATASE ...) x 3
KeywordsLYASE / beta-alpha-barrels
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 / : / 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: 1.85 Å
AuthorsShibata, N. / Masuda, J. / Morimoto, Y. / Yasuoka, N. / Toraya, T.
CitationJournal: Biochemistry / Year: 2002
Title: Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase
Authors: Shibata, N. / Masuda, J. / Morimoto, Y. / Yasuoka, N. / Toraya, T.
History
DepositionMay 1, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4May 31, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIOL DEHYDRATASE alpha chain
B: DIOL DEHYDRATASE beta chain
G: DIOL DEHYDRATASE gamma chain
L: DIOL DEHYDRATASE alpha chain
E: DIOL DEHYDRATASE beta chain
M: DIOL DEHYDRATASE gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,39214
Polymers207,4976
Non-polymers2,8958
Water17,330962
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27230 Å2
ΔGint-119 kcal/mol
Surface area51290 Å2
MethodPISA
2
B: DIOL DEHYDRATASE beta chain
hetero molecules

E: DIOL DEHYDRATASE beta chain
hetero molecules

A: DIOL DEHYDRATASE alpha chain
G: DIOL DEHYDRATASE gamma chain
L: DIOL DEHYDRATASE alpha chain
M: DIOL DEHYDRATASE gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,39214
Polymers207,4976
Non-polymers2,8958
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_755-x+5/2,-y,z+1/21
crystal symmetry operation2_654-x+3/2,-y,z-1/21
identity operation1_555x,y,z1
Buried area23840 Å2
ΔGint-95 kcal/mol
Surface area57050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.79, 122.40, 207.59
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 DEHYDRATASE ... , 3 types, 6 molecules ALBEGM

#1: Protein DIOL DEHYDRATASE alpha chain


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


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


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

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Non-polymers , 3 types, 970 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 962 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8
Details: PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, 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-IDDetailsChemical formula
150 mg/mlenzyme1drop
210 mMpotassium phosphate1droppH8.0
30.10 %LDAO1drop
420000 nMCN-Cbl1drop
515 %(w/v)PEG60001reservoir
60.24 M1reservoirLiCl
720 mMTris-HCl1reservoirpH8.0

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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: 1.85→50 Å / Num. all: 1656266 / Num. obs: 126694 / % possible obs: 76.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.92 Å / % possible all: 53.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 1656266 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 53.6 % / Rmerge(I) obs: 0.176

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 6341 RANDOM
Rwork0.181 --
obs0.181 120342 -
all-120342 -
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13296 0 188 962 14446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_from_restr_planes0.34
X-RAY DIFFRACTIONs_zero_chiral_vol0.028
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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