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- PDB-1iwp: Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 1iwp
TitleGlycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae
Components(Glycerol Dehydratase ...) x 3
KeywordsLYASE / B12 / GLYCEROL DEHYDRATASE / KLEBSIELLA PNEUMONIAE / COBALAMIN / RADICAL CATALYSIS
Function / homology
Function and homology information


glycerol dehydratase / glycerol dehydratase activity / propanediol dehydratase / propanediol dehydratase activity / cobalamin 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 / Glycerol dehydrase beta subunit / Glycerol dehydrase gamma subunit / Glycerol dehydrase alpha subunit
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYamanishi, M. / Yunoki, M. / Tobimatsu, T. / Toraya, T.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.
Authors: Yamanishi, M. / Yunoki, M. / Tobimatsu, T. / Sato, H. / Matsui, J. / Dokiya, A. / Iuchi, Y. / Oe, K. / Suto, K. / Shibata, N. / Morimoto, Y. / Yasuoka, N. / Toraya, T.
History
DepositionMay 28, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2002Provider: 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 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Glycerol Dehydratase Alpha subunit
B: Glycerol Dehydratase Beta subunit
G: Glycerol Dehydratase Gamma subunit
L: Glycerol Dehydratase Alpha subunit
E: Glycerol Dehydratase Beta subunit
M: Glycerol Dehydratase Gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,34812
Polymers196,4576
Non-polymers2,8916
Water15,871881
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26360 Å2
ΔGint-130 kcal/mol
Surface area52250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.380, 108.223, 113.141
Angle α, β, γ (deg.)90.00, 96.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Glycerol Dehydratase ... , 3 types, 6 molecules ALBEGM

#1: Protein Glycerol Dehydratase Alpha subunit / glycerol dehydrase alpha subunit


Mass: 60714.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59476, glycerol dehydratase
#2: Protein Glycerol Dehydratase Beta subunit / glycerol dehydrase beta subunit


Mass: 21385.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E, pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: O08505, glycerol dehydratase
#3: Protein Glycerol Dehydratase Gamma subunit / glycerol dehydrase gamma subunit


Mass: 16128.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59475, glycerol dehydratase

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Non-polymers , 4 types, 887 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.: 881 / 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: 3.03 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion (sandwitch drop) / pH: 8
Details: 20mM Tris-HCl, 15% PEG6000, 0.2M Na2SO4, pH 8.0, VAPOR DIFFUSION (Sandwitch Drop), temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: sandwich-drop vapor diffusion / Details: Shibata, N., (1999) Structure, 7, 997.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG60001reservoir
20.24 Mammonium sulfate1reservoir
320 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.816 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.816 Å / Relative weight: 1
ReflectionResolution: 2→45.175 Å / Num. all: 130797 / Num. obs: 130797 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Rsym value: 0.132 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / % possible all: 97.6
Reflection
*PLUS
Num. obs: 130635 / Num. measured all: 958394 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.38

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB id, 1DIO

1dio


Resolution: 2.1→45 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 11285 10 %random
Rwork0.209 ---
all-113515 --
obs-113453 99.9 %-
Displacement parametersBiso mean: 28.73 Å2
Baniso -1Baniso -2Baniso -3
1--9.671 Å20 Å22.061 Å2
2---3.285 Å20 Å2
3---12.956 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13556 0 194 881 14631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0063
X-RAY DIFFRACTIONc_angle_deg1.32008
X-RAY DIFFRACTIONc_dihedral_angle_d21.48409
X-RAY DIFFRACTIONc_improper_angle_d0.88607
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3036 1151 10.16 %
Rwork0.2606 10179 -
Refinement
*PLUS
Lowest resolution: 45 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.48409
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88607
LS refinement shell
*PLUS
Rfactor Rfree: 0.3036 / Rfactor Rwork: 0.2606

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