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- PDB-1egm: CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. -

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Basic information

Entry
Database: PDB / ID: 1egm
TitleCRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K.
Components(PROPANEDIOL DEHYDRATASE) x 3
KeywordsLYASE / CYANOCOBALAMIN / 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
CYANOCOBALAMIN / : / 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 / Resolution: 1.85 Å
AuthorsMasuda, J. / Shibata, N. / Toraya, T. / Morimoto, Y. / Yasuoka, N.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Authors: Masuda, J. / Shibata, N. / Morimoto, Y. / Toraya, T. / Yasuoka, N.
#1: Journal: Structure / 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. / Toraya, T. / Morimoto, Y. / Yasuoka, N.
History
DepositionFeb 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
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 2.1Feb 7, 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: PROPANEDIOL DEHYDRATASE
B: PROPANEDIOL DEHYDRATASE
G: PROPANEDIOL DEHYDRATASE
L: PROPANEDIOL DEHYDRATASE
E: PROPANEDIOL DEHYDRATASE
M: PROPANEDIOL DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,44012
Polymers207,4976
Non-polymers2,9436
Water21,8161211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25620 Å2
ΔGint-119 kcal/mol
Surface area52660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.00, 121.6, 207.7
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is heterohexamer constructed from A, B, G, L, E, G chains and two cyanocobalamins.

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Components

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Protein , 3 types, 6 molecules ALBEGM

#1: Protein PROPANEDIOL DEHYDRATASE /


Mass: 60408.133 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59470, propanediol dehydratase
#2: Protein PROPANEDIOL DEHYDRATASE /


Mass: 24141.678 Da / Num. of mol.: 2 / Fragment: BETA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59471, propanediol dehydratase
#3: Protein PROPANEDIOL DEHYDRATASE /


Mass: 19198.695 Da / Num. of mol.: 2 / Fragment: GAMMA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59472, propanediol dehydratase

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Non-polymers , 4 types, 1217 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CNC / CYANOCOBALAMIN / Cyanocobalamin


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Comment: medication*YM
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1211 / 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: 45.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sandwich / pH: 8
Details: PEG6000, potassium phosphate, Tris, lauryldimethylamine oxide, ammonium sulfate, propane diol, cyanocobalamin, pH 8.0, VAPOR DIFFUSION, SANDWICH, temperature 277K
Crystal grow
*PLUS
Details: Masuda, J., (1999) Acta Crystallogr, D55, 907. / Method: vapor diffusion, sandwich drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl11
20.24 Mammonium sulfate11
315 %PEG600011
40.20 %LDAO11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 142052 / Num. obs: 142006 / % possible obs: 88.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.134 / Num. unique all: 5330 / % possible all: 67.7
Reflection
*PLUS
Num. obs: 142053 / Num. measured all: 1939544
Reflection shell
*PLUS
% possible obs: 67.7 %

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Processing

Software
NameVersionClassification
SHELXL-97refinement
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 1.85→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2491 7097 RANDOM
Rwork0.1817 --
obs0.1817 134925 -
all-142049 -
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13333 0 194 1214 14741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_bond_d0.006
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.243 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS

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