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- PDB-1mzo: Crystal structure of pyruvate formate-lyase with pyruvate -

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Basic information

Entry
Database: PDB / ID: 1mzo
TitleCrystal structure of pyruvate formate-lyase with pyruvate
ComponentsPyruvate formate-lyase
KeywordsTRANSFERASE / ENZYME-SUBSTRATE COMPLEX
Function / homology
Function and homology information


glycolytic fermentation via PFL pathway / 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. ...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
TRIETHYLENE GLYCOL / PYRUVIC ACID / Formate acetyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLehtio, L. / Leppanen, V.-M. / Kozarich, J.W. / Goldman, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of Escherichia coli pyruvate formate-lyase with pyruvate.
Authors: Lehtio, L. / Leppanen, V.M. / Kozarich, J.W. / Goldman, A.
History
DepositionOct 9, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate formate-lyase
B: Pyruvate formate-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9825
Polymers170,6562
Non-polymers3263
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-5 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.355, 158.355, 159.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1001-

PGE

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Components

#1: Protein Pyruvate formate-lyase / Formate acetyltransferase 1


Mass: 85327.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pKK223-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09373, formate C-acetyltransferase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.92 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7.3
Details: PEG1000, MOPS, ammonium chloride, na-pyruvate, DTT, magnesium chloride, EDTA, pH 7.3, MICRODIALYSIS, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMMOPS/NH311
220 mMdithiothreitol11
325 mg/mlprotein11
425 mMMOPS/NH312pH7.3
525 %(w/v)PEG100012
610 mMdithiothreitol12
725 mM12NH4Cl
825 mMsodium pyruvate12
91 mMEDTA12
102 mM12MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9102 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9102 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 56141 / Num. obs: 55923 / % possible obs: 98.8 % / Observed criterion σ(F): -1
Reflection shellResolution: 2.7→2.8 Å / % possible all: 94.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 318766 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PFL

2pfl


Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 9 OF THE POLYETHYLENE GLYCOL ATOMS WERE INCLUDED IN REFINEMENT AND ATOM O1 ADDED AFTERWARDS ON SYMMETRY AXIS WITH 0.5 OCCUPANCY
RfactorNum. reflectionSelection details
Rfree0.235 2715 RANDOM
Rwork0.196 --
all-55923 -
obs-55885 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11930 0 22 515 12467
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.2
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg21.5
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.72

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