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- PDB-1h16: Pyruvate Formate-Lyase (E.coli) in complex with Pyruvate and CoA -

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Basic information

Entry
Database: PDB / ID: 1h16
TitlePyruvate Formate-Lyase (E.coli) in complex with Pyruvate and CoA
ComponentsFORMATE ACETYLTRANSFERASE 1
KeywordsTRANSFERASE / LYASE / GLYCYL RADICAL ENZYME / ACYLTRANSFERASE
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
COENZYME A / L-TREITOL / PYRUVIC ACID / Formate acetyltransferase 1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBecker, A. / Kabsch, W.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: X-Ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and Coa.How the Enzyme Uses the Cys-418 Thiyl Radical for Pyruvate Cleavage
Authors: Becker, A. / Kabsch, W.
History
DepositionJul 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2002Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMATE ACETYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,19616
Polymers85,3281
Non-polymers1,86815
Water22,8251267
1
A: FORMATE ACETYLTRANSFERASE 1
hetero molecules

A: FORMATE ACETYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,39132
Polymers170,6562
Non-polymers3,73530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)54.900, 153.050, 205.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2226-

HOH

21A-2502-

HOH

31A-2594-

HOH

41A-3228-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FORMATE ACETYLTRANSFERASE 1 / PYRUVATE FORMATE-LYASE


Mass: 85327.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMPLEX OF PYRUVATE FORMATE-LYASE WITH ITS SUBSTRATES PYRUVATE AND COA
Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P09373, formate C-acetyltransferase

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Non-polymers , 7 types, 1282 molecules

#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DTL / L-TREITOL


Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1267 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsGLUCOSE NONOXIDATIVE CONVERSION METABOLISM PATHWAY. ACETYL-COA + FORMATE = COA + PYRUVATE.

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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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growpH: 7.3 / Details: pH 7.30
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
225 mMMOPS/NaOH1droppH7.3
350 mMsodium oxamate1dropor sodium pyruvate
43 mM1dropCaA:Li3
51 mMdithiothreitol1drop
61 mMEDTA1drop
73 mM1dropNaN3
813 %(w/v)PEG5000 MME1drop
922 %(w/v)PEG5000 MME1reservoir
1050 mM1reservoirpH7.5kH2PO4/KOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8045
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8045 Å / Relative weight: 1
ReflectionResolution: 1.53→15 Å / Num. obs: 128878 / % possible obs: 98.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 28.93
Reflection shellResolution: 1.53→1.6 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 7.52 / % possible all: 89.8
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 1104993 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 89.8 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 7.5

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PFL

3pfl


Resolution: 1.53→15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5042753.84 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: ELECTRON DENSITY NEAR PHOSPHATES OF COA WAS EXPLAINED AS MG2+ ALTHOUGH NO DIVALENT CATIONS WERE INCLUDED IN THE CRYSTALLIZATION BUFFER
RfactorNum. reflection% reflectionSelection details
Rfree0.163 2576 2 %RANDOM
Rwork0.145 ---
obs0.145 128782 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6765 Å2 / ksol: 0.370898 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 117 1267 7372
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.931.5
X-RAY DIFFRACTIONc_mcangle_it1.342
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.482.5
LS refinement shellResolution: 1.53→1.63 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.223 398 2 %
Rwork0.204 19479 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_1.8.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3COAACO.PARCOAACO.TOP
X-RAY DIFFRACTION4PYR_XPLOR+DTR+LTR+PEG1.PARPYR_XPLOR+DTR+LTR+PEG1.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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