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- PDB-3c8f: 4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially di... -

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Basic information

Entry
Database: PDB / ID: 3c8f
Title4Fe-4S-Pyruvate formate-lyase Activating Enzyme with partially disordered AdoMet
ComponentsPyruvate formate-lyase 1-activating enzyme
KeywordsOXIDOREDUCTASE / AdoMet radical / SAM radical / activase / glycyl radical / Carbohydrate metabolism / Glucose metabolism / Iron / Iron-sulfur / Metal-binding / S-adenosyl-L-methionine
Function / homology
Function and homology information


[formate-C-acetyltransferase]-activating enzyme / [formate-C-acetyltransferase]-activating enzyme activity / potassium ion binding / protein maturation / glucose metabolic process / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / DNA damage response / cytosol
Similarity search - Function
Pyruvate formate-lyase 1 activating enzyme / Radical-activating enzyme, conserved site / Organic radical enzyme activase / Organic radical-activating enzymes / Pyruvate formate-lyase activase / Radical activating enzymes signature. / 4Fe-4S single cluster domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM ...Pyruvate formate-lyase 1 activating enzyme / Radical-activating enzyme, conserved site / Organic radical enzyme activase / Organic radical-activating enzymes / Pyruvate formate-lyase activase / Radical activating enzymes signature. / 4Fe-4S single cluster domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-MT2 / TRIETHYLENE GLYCOL / IRON/SULFUR CLUSTER / Pyruvate formate-lyase 1-activating enzyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsVey, J.L. / Drennan, C.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.
Authors: Vey, J.L. / Yang, J. / Li, M. / Broderick, W.E. / Broderick, J.B. / Drennan, C.L.
History
DepositionFeb 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 14, 2014Group: Atomic model
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 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: Pyruvate formate-lyase 1-activating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7954
Polymers28,1151
Non-polymers6803
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.051, 58.051, 117.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Pyruvate formate-lyase 1-activating enzyme / PFL-activating enzyme / Formate-C-acetyltransferase-activating enzyme 1


Mass: 28115.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pflA / Plasmid: pCAL-n-AE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P0A9N4, [formate-C-acetyltransferase]-activating enzyme
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MT2 / [(3S)-3-amino-3-carboxypropyl](ethyl)methylsulfonium / S-ethyl-L-Methionine


Type: L-peptide linking / Mass: 178.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO2S
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M tris, 25% PEG 3350, 0.11 mM octaethylene glycol monododecyl ether, pH 8.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-111.73542, 1.74166, 1.37755
SYNCHROTRONSSRL BL9-121
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 4, 2005Inter-frame total dead time: 3s
ADSC QUANTUM 3152CCDJun 4, 2005Inter-frame total dead time: 3s
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 degsMADMx-ray1
2Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 degsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.735421
21.741661
31.377551
411
ReflectionRedundancy: 7.3 % / Av σ(I) over netI: 16.8 / Number: 104757 / Rmerge(I) obs: 0.09 / Χ2: 0.98 / D res high: 2.87 Å / D res low: 100 Å / Num. obs: 9997 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.1810094.210.0621.0186.8
4.916.1894.910.0761.0387
4.294.9189.610.0871.0047.4
3.94.2996.510.1031.057.6
3.623.998.810.1261.0577.7
3.43.6210010.1521.0037.7
3.233.499.910.1680.9467.7
3.093.2310010.2230.9087.6
2.973.0910010.2770.8877.3
2.872.9798.710.380.8436.6
ReflectionResolution: 2.25→30.9 Å / Num. obs: 11200 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.093 / Χ2: 1.019 / Net I/σ(I): 21.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1115 / Rsym value: 0.44 / Χ2: 0.989 / % possible all: 98.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.05phasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→30.9 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1010 8.9 %Random
Rwork0.224 ---
obs0.239 10618 93.1 %-
all-10618 --
Solvent computationBsol: 55.306 Å2
Displacement parametersBiso mean: 57.985 Å2
Baniso -1Baniso -2Baniso -3
1-1.461 Å2-2.438 Å20 Å2
2--1.461 Å20 Å2
3----2.921 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 29 60 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4411.5
X-RAY DIFFRACTIONc_scbond_it2.0952
X-RAY DIFFRACTIONc_mcangle_it2.3972
X-RAY DIFFRACTIONc_scangle_it3.2052.5
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.65
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 147 9.3 %
Rwork0.275 1428 -
obs-1428 85.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ligands3.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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