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- PDB-4mtj: Structure of the b12-independent glycerol dehydratase with 1,2-pr... -

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Basic information

Entry
Database: PDB / ID: 4mtj
TitleStructure of the b12-independent glycerol dehydratase with 1,2-propanediol bound
ComponentsB12-independent glycerol dehydratase
KeywordsHYDROLASE / PFL-like glycyl radical enzyme / glycerol/diol dehydratase
Function / homology
Function and homology information


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 ...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
S-1,2-PROPANEDIOL / Glycerol dehydratase
Similarity search - Component
Biological speciesClostridium butyricum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLaMattina, J. / Wright, A.V. / Demick, J. / Soucaille, P. / Lanzilotta, W.N.
CitationJournal: To be Published
Title: When Computational Chemistry and Modern Software Get It Right; New Insight Into the Mechanism of a Glycyl Radical Enzyme
Authors: LaMattina, J. / Wright, A.V. / Demick, J. / Soucaille, P. / Lanzilotta, W.N.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionOct 9, 2013ID: 1R9E
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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: B12-independent glycerol dehydratase
B: B12-independent glycerol dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,4624
Polymers176,3092
Non-polymers1522
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-10 kcal/mol
Surface area51040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.696, 212.399, 198.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein B12-independent glycerol dehydratase / Glycerol dehydratase


Mass: 88154.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium butyricum (bacteria) / Gene: dhaB1 / References: UniProt: Q8GEZ8
#2: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


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


Mass: 18.015 Da / Num. of mol.: 896 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growMethod: evaporation / pH: 6.5
Details: PEG 3350, TRI-AMMONIUM CITRATE, CAPILLARY BATCH, pH 6.5, EVAPORATION

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 86724 / Num. obs: 83283 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1R9E

1r9e
PDB Unreleased entry


Resolution: 2.4→46.228 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 4162 5.01 %random
Rwork0.1701 ---
obs0.1724 83145 97.87 %-
all-83283 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12380 0 10 896 13286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812632
X-RAY DIFFRACTIONf_angle_d1.06517052
X-RAY DIFFRACTIONf_dihedral_angle_d14.2924740
X-RAY DIFFRACTIONf_chiral_restr0.0741856
X-RAY DIFFRACTIONf_plane_restr0.0052238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.26621210.22092276X-RAY DIFFRACTION85
2.4273-2.45580.26511270.21562379X-RAY DIFFRACTION89
2.4558-2.48580.27751410.20542418X-RAY DIFFRACTION91
2.4858-2.51720.25681220.20422478X-RAY DIFFRACTION94
2.5172-2.55040.28221430.20082533X-RAY DIFFRACTION95
2.5504-2.58530.2821420.21032561X-RAY DIFFRACTION97
2.5853-2.62220.25741470.21092652X-RAY DIFFRACTION98
2.6222-2.66140.28271320.20272589X-RAY DIFFRACTION99
2.6614-2.70290.22991360.19482620X-RAY DIFFRACTION98
2.7029-2.74730.23491370.1862650X-RAY DIFFRACTION99
2.7473-2.79460.23821430.18542652X-RAY DIFFRACTION99
2.7946-2.84540.26391380.18292659X-RAY DIFFRACTION99
2.8454-2.90020.25931270.1832639X-RAY DIFFRACTION99
2.9002-2.95930.231570.18192665X-RAY DIFFRACTION100
2.9593-3.02370.24761390.18382696X-RAY DIFFRACTION99
3.0237-3.0940.23541450.18562624X-RAY DIFFRACTION99
3.094-3.17140.25011430.19522656X-RAY DIFFRACTION100
3.1714-3.25710.23881620.19282646X-RAY DIFFRACTION100
3.2571-3.35290.25981250.19182706X-RAY DIFFRACTION100
3.3529-3.46110.24561480.19262668X-RAY DIFFRACTION100
3.4611-3.58470.19781550.17762669X-RAY DIFFRACTION100
3.5847-3.72820.23121170.16552717X-RAY DIFFRACTION100
3.7282-3.89780.17921450.15542672X-RAY DIFFRACTION100
3.8978-4.10320.17261500.14782698X-RAY DIFFRACTION100
4.1032-4.36010.1841420.1442706X-RAY DIFFRACTION100
4.3601-4.69640.17741460.13552709X-RAY DIFFRACTION100
4.6964-5.16850.17741250.13442733X-RAY DIFFRACTION100
5.1685-5.91510.16791230.13922761X-RAY DIFFRACTION100
5.9151-7.44730.16951460.14182755X-RAY DIFFRACTION100
7.4473-46.23660.13421380.13582796X-RAY DIFFRACTION97

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