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- PDB-1mmf: Crystal structure of substrate free form of glycerol dehydratase -

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Basic information

Entry
Database: PDB / ID: 1mmf
TitleCrystal structure of substrate free form of glycerol dehydratase
Components(glycerol dehydrase ...) x 3
KeywordsLYASE / Glycerol dehydratase / Diol dehydratase / Coenzyme B12 / TIM barrel
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 / : / 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: 2.5 Å
AuthorsLiao, D.I. / Dotson, G. / Turner, I. / Reiss, L. / Emptage, M.
CitationJournal: J.Inorg.Biochem. / Year: 2003
Title: Crystal structure of substrate free form of glycerol dehydratase
Authors: Liao, D.I. / Dotson, G. / Turner, I. / Reiss, L. / Emptage, M.
History
DepositionSep 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: 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_ref_seq_dif / 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_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_ref_seq_dif.details / _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 dehydrase alpha subunit
B: glycerol dehydrase beta subunit
G: glycerol dehydrase gamma subunit
L: glycerol dehydrase alpha subunit
E: glycerol dehydrase beta subunit
M: glycerol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,13210
Polymers196,3936
Non-polymers2,7394
Water3,729207
1
A: glycerol dehydrase alpha subunit
B: glycerol dehydrase beta subunit
G: glycerol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5665
Polymers98,1963
Non-polymers1,3692
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-47 kcal/mol
Surface area31310 Å2
MethodPISA
2
L: glycerol dehydrase alpha subunit
E: glycerol dehydrase beta subunit
M: glycerol dehydrase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5665
Polymers98,1963
Non-polymers1,3692
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-48 kcal/mol
Surface area31850 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26150 Å2
ΔGint-132 kcal/mol
Surface area54480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.70, 110.07, 114.69
Angle α, β, γ (deg.)90.00, 107.64, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biologyical assembly of glycerol dehydratase is a heterohexamer. It is a dimer of alpha-beta-gamma trimers. The asymmetric unit in the crystal contains an entire heterohexamer. Chain names for subunits are A, B, and G fare one trimer and L, E and M for the second trimer.

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Components

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

#1: Protein glycerol dehydrase alpha subunit / glycerol dehydratase alpha subunit


Mass: 60714.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pBluescript SKII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q59476, glycerol dehydratase
#2: Protein glycerol dehydrase beta subunit / glycerol dehydratase beta subunit


Mass: 21353.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pBluescript SKII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O08505, glycerol dehydratase
#3: Protein glycerol dehydrase gamma subunit / glycerol dehydratase gamma subunit


Mass: 16128.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pBluescript SKII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q59475, glycerol dehydratase

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Non-polymers , 3 types, 211 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / 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.: 207 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: Amonium sulfate, RbCl2, CdCl2, cyanocobalamin, CHES, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.1-1.3 Mammonium sulfate1reservoir
20.2 M1reservoirRbCl
30.2 mM1reservoirCdCl2
40.2 Mcyanocobalamin1reservoir
50.1 MCHES-KOH1reservoirpH9.4-9.7
68 mg/mlprotein1drop
750 mMHEPES-KOH1droppH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 67426 / Num. obs: 67426 / % possible obs: 87.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.1 / % possible all: 50.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 302300
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 50.1 % / Rmerge(I) obs: 0.14

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DIO

1dio


Resolution: 2.5→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.269 3246
Rwork0.228 -
all-67426
obs-64004
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13391 0 184 207 13782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_bond_d0.008
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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