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- PDB-1qhm: ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1qhm
TitleESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN
ComponentsPYRUVATE FORMATE-LYASE
KeywordsLYASE/TRANSFERASE / PYRUVATE FORMATE LYASE / ANAEROBIC / HOMODIMER / ENZYME MECHANISM / LYASE-TRANSFERASE COMPLEX
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 / MIRAS / Resolution: 2.8 Å
AuthorsLeppanen, V.-M. / Merckel, M.C. / Ollis, D.L. / Wong, K.K. / Kozarich, J.W. / Goldman, A.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase.
Authors: Leppanen, V.M. / Merckel, M.C. / Ollis, D.L. / Wong, K.K. / Kozarich, J.W. / Goldman, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification and Crystallization of a Proteolytic Fragment of Escherichia coli Pyruvate Formate-Lyase
Authors: Leppanen, V.-M. / Parast, C.V. / Wong, K.K. / Kozarich, J.W. / Goldman, A.
History
DepositionMay 19, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)141,0782
Polymers141,0782
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-12 kcal/mol
Surface area46940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.800, 140.800, 215.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.991906, -0.126812, -0.006467), (-0.125856, 0.975127, 0.182451), (-0.01683, 0.181788, -0.983194)
Vector: 161.58018, 1.88095, 92.5545)

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Components

#1: Protein PYRUVATE FORMATE-LYASE / PFL


Mass: 70539.180 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Gene: PFL / Plasmid: PKK-TRYPFL / Species (production host): Escherichia coli / Gene (production host): PFL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09373, formate C-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 4.4 Å3/Da / Density % sol: 72 %
Description: IN ADDITION TO THE MIRAS DATA, A SEMET SUBSTITUENT AND MERCURY MAD DATA WERE COLLECTED ON THE BEAMLINE BW7A AT EMBL-HAMBURG OUTSTATION
Crystal growpH: 7.6
Details: 18% PEG-1000, 0.1 M HEPES/HCL PH7.6, VAPOUR DIFFUSION
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, sitting drop
Details: Leppanen, V.-M., (1999) Acta Crystallogr., Sect.D, 55, 531.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130-50 mg/mlprotein1drop
2100 mMHEPES-HCl1reservoirpH7.6
318-24 %(w/v)PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorDetector: CCD / Date: May 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 59411 / % possible obs: 99.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 56.6 Å2 / Rsym value: 5.2 / Net I/σ(I): 22.5
Reflection shellResolution: 2.8→2.86 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 43.7 / % possible all: 99.2
Reflection
*PLUS
Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2705139.55 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 5344 9.1 %RANDOM
Rwork0.228 ---
obs-58723 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 63.4 Å2
Baniso -1Baniso -2Baniso -3
1-14.392 Å217.563 Å20 Å2
2--14.392 Å20 Å2
3----28.784 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9576 0 0 234 9810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.88 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.408 389 8 %
Rwork0.376 4491 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.1 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 63.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.408 / % reflection Rfree: 8 % / Rfactor Rwork: 0.376

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