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- PDB-2f3o: Crystal Structure of a glycyl radical enzyme from Archaeoglobus f... -

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Basic information

Entry
Database: PDB / ID: 2f3o
TitleCrystal Structure of a glycyl radical enzyme from Archaeoglobus fulgidus
Componentspyruvate formate-lyase 2
KeywordsUNKNOWN FUNCTION / pyruvate formate lyase / glycerol dehydratase / PFL2 / glycyl radical / hyperthermophilic
Function / homology
Function and homology information


lyase activity / cytosol
Similarity search - Function
Glycyl radical enzyme, PFL2/glycerol dehydratase family / : / 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 ...Glycyl radical enzyme, PFL2/glycerol dehydratase family / : / 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
TRIETHYLENE GLYCOL / Pyruvate formate-lyase 2 (PflD)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLehtio, L. / Goldman, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of a glycyl radical enzyme from Archaeoglobus fulgidus
Authors: Lehtio, L. / Grossmann, J.G. / Kokona, B. / Fairman, R. / Goldman, A.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: pyruvate formate-lyase 2
B: pyruvate formate-lyase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,0136
Polymers174,5292
Non-polymers4854
Water3,009167
1
A: pyruvate formate-lyase 2
hetero molecules

A: pyruvate formate-lyase 2
hetero molecules

A: pyruvate formate-lyase 2
hetero molecules

A: pyruvate formate-lyase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,02712
Polymers349,0584
Non-polymers9698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
2
B: pyruvate formate-lyase 2
hetero molecules

B: pyruvate formate-lyase 2
hetero molecules

B: pyruvate formate-lyase 2
hetero molecules

B: pyruvate formate-lyase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,02712
Polymers349,0584
Non-polymers9698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_457-x-1,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Unit cell
Length a, b, c (Å)167.030, 174.170, 162.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

21B-810-

HOH

31B-814-

HOH

41B-831-

HOH

DetailsThe biological tetramer is formed from chain A with symmetry operators: -x, -y+1, z x, -y+1, -z+1 -x, y, -z+1 / The biological tetramer is formed from chain B with symmetry operators: x, -y+1, -z -x-1, -y+1, z -x-1, y, -z+2

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Components

#1: Protein pyruvate formate-lyase 2 / pflD / PFL2


Mass: 87264.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1449, PFLD / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O28823
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.38 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16 % PEG8000, 8 % isopropanol, 80 mM Hepes pH 7.5, 160 mM ammonium sulphate, 1 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 52531 / Num. obs: 52531 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.61
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 5.34 / Num. unique all: 36376 / Num. unique obs: 4896 / % possible all: 97.2

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.185 / Packing: 0.427
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation3.5 Å30 Ågeneral99.5 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
CNSrefinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1R9D

1r9d


Resolution: 2.9→19.69 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.048 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 4.668 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2648 5 %RANDOM
Rwork0.199 ---
all0.202 52529 --
obs0.202 52529 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12222 0 32 167 12421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212482
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.97316872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.51251544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42224.276594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.559152206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1381592
X-RAY DIFFRACTIONr_chiral_restr0.1160.21866
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029460
X-RAY DIFFRACTIONr_nbd_refined0.1580.16560
X-RAY DIFFRACTIONr_nbtor_refined0.3240.58563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.1738
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.177
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.117
X-RAY DIFFRACTIONr_mcbond_it0.4761.57810
X-RAY DIFFRACTIONr_mcangle_it0.864212378
X-RAY DIFFRACTIONr_scbond_it1.08135167
X-RAY DIFFRACTIONr_scangle_it1.8934.54494
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 203 -
Rwork0.308 3576 -
obs-3779 100 %

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