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- PDB-1cm5: CRYSTAL STRUCTURE OF C418A,C419A MUTANT OF PFL FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 1cm5
TitleCRYSTAL STRUCTURE OF C418A,C419A MUTANT OF PFL FROM E.COLI
ComponentsPROTEIN (PYRUVATE FORMATE-LYASE)
KeywordsTRANSFERASE / GLYCYL RADICAL ENZYME / GLUCOSE METABOLISM
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
CARBONATE ION / Formate acetyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 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 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)170,6946
Polymers170,5282
Non-polymers1664
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-37 kcal/mol
Surface area48860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.059, 159.059, 159.784
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: (-0.911, 0.4079, 0.0612), (0.4092, 0.8749, 0.2592), (0.0522, 0.2612, -0.9639)
Vector: 131.2207, -52.4031, 171.8981)

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Components

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


Mass: 85263.773 Da / Num. of mol.: 2 / Mutation: C418A,C419A / Source method: isolated from a natural source
Details: UNKNOWN DENSITY IN ACTIVE SITE OF EACH MONOMER WAS MODELLED AS CARBONATE
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P09373, formate C-acetyltransferase
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#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.: 740 / 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: 2.97 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/mlprotein11
225 mMMops/NH311
350 mM11NH4Cl
410 mMdithiothreitol11
53 mM11NaN3
616 %(w/v)PEG100011
725 mMMops/NH312
850 mM12NH4Cl
91 mMdithiothreitol12
101 mMEDTA12
113 mM12NaN3
122 mM12MgCl2
1324-30 %(w/v)PEG100012

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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: 2.3→20 Å / Num. obs: 87117 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 52.7 Å2 / Rmerge(I) obs: 0.07
Reflection
*PLUS
Num. measured all: 469884

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Processing

Software
NameVersionClassification
CNS0.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 520387.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS (RESIDUES A1-A3 AND B1-B3) WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4356 5 %RANDOM
Rwork0.216 ---
obs0.216 87117 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.89 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å20 Å2
2--1.66 Å20 Å2
3----3.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12001 0 10 740 12751
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_deg1.3
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_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 720 5 %
Rwork0.294 13695 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CO3.PARCO3.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_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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