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- PDB-1r9d: Glycerol bound form of the B12-independent glycerol dehydratase f... -

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Basic information

Entry
Database: PDB / ID: 1r9d
TitleGlycerol bound form of the B12-independent glycerol dehydratase from Clostridium butyricum
Componentsglycerol dehydratase
KeywordsLYASE / glycerol dehydratase / radical SAM
Function / homology
Function and homology information


lyase activity / cytosol
Similarity search - Function
Glycyl radical enzyme, PFL2/glycerol dehydratase family / : / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. ...Glycyl radical enzyme, PFL2/glycerol dehydratase family / : / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glycerol dehydratase
Similarity search - Component
Biological speciesClostridium butyricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLanzilotta, W.N. / O'Brien, J.R. / Raynaud, C. / Soucaille, P.
CitationJournal: Biochemistry / Year: 2004
Title: Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization.
Authors: O'Brien, J.R. / Raynaud, C. / Croux, C. / Girbal, L. / Soucaille, P. / Lanzilotta, W.N.
History
DepositionOct 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: glycerol dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,4944
Polymers176,3092
Non-polymers1842
Water17,457969
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-21 kcal/mol
Surface area51940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.092, 213.420, 199.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe file contains the asymmetric unit, which is also proposed to be the physiological dimer

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Components

#1: Protein glycerol dehydratase


Mass: 88154.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium butyricum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GEZ8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 270 K / Method: capillary batch / pH: 6.5
Details: PEG 3350, tri-ammonium citrate, pH 6.5, capillary batch, temperature 270K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 199038 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.08 / Net I/σ(I): 26.7
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.28 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 4580453.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 9995 5 %RANDOM
Rwork0.217 ---
all0.217 ---
obs0.217 198857 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.813 Å2 / ksol: 0.34568 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.44 Å20 Å20 Å2
2---8.32 Å20 Å2
3---0.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12380 0 12 969 13361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it0.771.5
X-RAY DIFFRACTIONc_mcangle_it1.182
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.22.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 1530 5 %
Rwork0.284 29294 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HETERO.PARAMHETERO.TOP

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