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- PDB-2pfl: CRYSTAL STRUCTURE OF PFL FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 2pfl
TitleCRYSTAL STRUCTURE OF PFL FROM E.COLI
ComponentsPROTEIN (PYRUVATE FORMATE-LYASE)
KeywordsLYASE / GLYCYL RADICAL ENZYME / TRANSFERASE / GLUCOSE METABOLISM
Function / homology
Function and homology information


formate C-acetyltransferase / formate C-acetyltransferase activity / glucose metabolic process / membrane / cytosol
Similarity search - Function
Formate acetyltransferase / 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 ...Formate acetyltransferase / 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
Formate acetyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBecker, A. / Fritz-Wolf, K. / Kabsch, W. / Knappe, J. / Schultz, S. / Wagner, A.F.V.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase.
Authors: Becker, A. / Fritz-Wolf, K. / Kabsch, W. / Knappe, J. / Schultz, S. / Volker Wagner, A.F.
History
DepositionMay 26, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 15, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: PROTEIN (PYRUVATE FORMATE-LYASE)
B: PROTEIN (PYRUVATE FORMATE-LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,7736
Polymers170,6562
Non-polymers1174
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-59 kcal/mol
Surface area48860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)159.020, 159.020, 160.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.912, 0.4057, 0.06), (0.4068, 0.8762, 0.2583), (0.0522, 0.26, -0.9642)
Vector: 131.4321, -52.2691, 172.97569)

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Components

#1: Protein PROTEIN (PYRUVATE FORMATE-LYASE) / PFL


Mass: 85327.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P09373, formate C-acetyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsEACH CHAIN OF THE HOMODIMER WAS MODELED WITH ONE CHLORIDE

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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: 2.97 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.3 / Details: pH 7.3
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMMops/NH31drop
350 mM1dropNH4Cl
410 mMdithiothreitol1drop
53 mM1dropNaN3
616 %(w/v)PEG10001drop
725 mMMops/NH31reservoir
850 mM1reservoirNH4Cl
91 mMdithiothreitol1reservoir
101 mMEDTA1reservoir
113 mM1reservoirNaN3
122 mM1reservoirMgCl2
1324-30 %(w/v)PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8467
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8467 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 45502 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.088
Reflection
*PLUS
Num. measured all: 186926

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 558066.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS (RESIDUES A1-A3 AND B1-B3) WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 2161 4.7 %RANDOM
Rwork0.2024 ---
obs-45198 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.23 Å2 / ksol: 0.2903 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.205 Å20 Å20 Å2
2---0.205 Å20 Å2
3---0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11976 0 4 742 12722
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.7861.5
X-RAY DIFFRACTIONc_mcangle_it1.0512
X-RAY DIFFRACTIONc_scbond_it1.3812
X-RAY DIFFRACTIONc_scangle_it1.6972.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 358 4.7 %
Rwork0.305 7193 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.paramPROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:water.paramWATER.TOP
X-RAY DIFFRACTION3oxm.par
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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