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- PDB-5i2a: 1,2-propanediol Dehydration in Roseburia inulinivorans; Structura... -

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Basic information

Entry
Database: PDB / ID: 5i2a
Title1,2-propanediol Dehydration in Roseburia inulinivorans; Structural Basis for Substrate and Enantiomer Selectivity
ComponentsDiol-dehydratase
KeywordsLYASE / diol dehydratase / glycyl radical enzymes / enzyme structure
Function / homology
Function and homology information


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 ...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
DI(HYDROXYETHYL)ETHER / Glycerol dehydratase
Similarity search - Component
Biological speciesRoseburia inulinivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLaMattina, J.W. / Reitzer, P. / Kapoor, S. / Galzerani, F. / Koch, D.J. / Gouvea, I.E. / Lanzilotta, W.N.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: 1,2-Propanediol Dehydration in Roseburia inulinivorans: STRUCTURAL BASIS FOR SUBSTRATE AND ENANTIOMER SELECTIVITY.
Authors: LaMattina, J.W. / Keul, N.D. / Reitzer, P. / Kapoor, S. / Galzerani, F. / Koch, D.J. / Gouvea, I.E. / Lanzilotta, W.N.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references / Structure summary
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diol-dehydratase
B: Diol-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,8849
Polymers188,2292
Non-polymers6557
Water21,4561191
1
A: Diol-dehydratase
hetero molecules

A: Diol-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,99010
Polymers188,2292
Non-polymers7618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area4700 Å2
ΔGint6 kcal/mol
Surface area54890 Å2
MethodPISA
2
B: Diol-dehydratase
hetero molecules

B: Diol-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,7788
Polymers188,2292
Non-polymers5496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area4150 Å2
ΔGint2 kcal/mol
Surface area55130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.206, 183.225, 228.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Diol-dehydratase / B12-independent or GRE-type dehydratase


Mass: 94114.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia inulinivorans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1A666
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1191 / 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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.125 M sodium acetate, 42 % PEG 400 (w/v), and 0.025 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 15, 2014
RadiationMonochromator: 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 168058 / % possible obs: 98.9 % / Redundancy: 6.3 % / Rsym value: 0.063 / Net I/σ(I): 22.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.8 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIXdev_1639refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.1→39.926 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.47
RfactorNum. reflection% reflection
Rfree0.1834 8337 5.02 %
Rwork0.1519 --
obs0.1535 165984 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.71 Å2 / Biso mean: 23.16 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 2.1→39.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13083 0 43 1191 14317
Biso mean--32.22 27.45 -
Num. residues----1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713492
X-RAY DIFFRACTIONf_angle_d1.01318256
X-RAY DIFFRACTIONf_chiral_restr0.0411982
X-RAY DIFFRACTIONf_plane_restr0.0062397
X-RAY DIFFRACTIONf_dihedral_angle_d13.9215021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.25042070.21244574478186
2.1239-2.14890.22262600.19334816507692
2.1489-2.17510.22262850.18724953523894
2.1751-2.20260.22022390.18725174541397
2.2026-2.23160.21122960.18275151544799
2.2316-2.26220.22282650.17953025567100
2.2622-2.29450.23033010.180552515552100
2.2945-2.32870.2142820.169452545536100
2.3287-2.36510.21622940.162852455539100
2.3651-2.40390.18972860.157552815567100
2.4039-2.44530.22442950.154952645559100
2.4453-2.48980.19872800.156153145594100
2.4898-2.53770.20732740.156452495523100
2.5377-2.58940.20422620.158353265588100
2.5894-2.64570.1992950.15752645559100
2.6457-2.70730.17612710.163353045575100
2.7073-2.7750.19362770.156353065583100
2.775-2.850.18022610.160152965557100
2.85-2.93380.21222780.163853455623100
2.9338-3.02850.20112850.166652725557100
3.0285-3.13670.22492700.171353135583100
3.1367-3.26220.21563030.174553025605100
3.2622-3.41060.19462730.174953315604100
3.4106-3.59030.17062670.161353705637100
3.5903-3.81510.16642900.139553285618100
3.8151-4.10940.14313010.124353185619100
4.1094-4.52240.15452780.115253435621100
4.5224-5.17560.14112950.111653865681100
5.1756-6.51610.1482800.128454385718100
6.5161-39.93340.13552870.124455775864100

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