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1mzo

Crystal structure of pyruvate formate-lyase with pyruvate

Method: X-RAY DIFFRACTION Dmax: 122.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyruvate formate-lyase

Escherichia coli

UniProt P09373

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–759 Chain B； UniProt 1–759 Not recorded PGE TRIETHYLENE GLYCOL × 1 PYR PYRUVIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions：MICRODIALYSIS；pH 7.3；298 K；PEG1000, MOPS, ammonium chloride, na-pyruvate, DTT, magnesium chloride, EDTA, pH 7.3, MICRODIALYSIS, temperature 298K Resolution 2.70 Å R-free 0.235

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1MZO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CM5 CRYSTAL STRUCTURE OF C418A,C419A MUTANT OF PFL FROM E.COLI Deposited 1999-05-14 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–759（759 aa）
Chain B 1–759（759 aa）
Mutation：C418A,C419A Mutation：C418A,C419A CO3 CARBONATE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.3
Resolution 2.30 Å R-free 0.251
1H16 Pyruvate Formate-Lyase (E.coli) in complex with Pyruvate and CoA Deposited 2002-07-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–759（759 aa）
Not recorded COA COENZYME A × 2 PYR PYRUVIC ACID × 2 NA SODIUM ION × 14 MG MAGNESIUM ION × 2 DTL L-TREITOL × 4 PG4 TETRAETHYLENE GLYCOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.30
Resolution 1.53 Å R-free 0.163
1H17 Pyruvate Formate-Lyase (E.coli) in complex with CoA and the substrate analog oxamate Deposited 2002-07-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–759（759 aa）
Not recorded COA COENZYME A × 2 OXM OXAMIC ACID × 2 NA SODIUM ION × 14 MG MAGNESIUM ION × 2 DTL L-TREITOL × 4 PG4 TETRAETHYLENE GLYCOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.30
Resolution 1.75 Å R-free 0.173
1H18 Pyruvate Formate-Lyase (E.coli) in complex with Pyruvate Deposited 2002-07-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–759（759 aa）
Chain B 1–759（759 aa）
Not recorded PYR PYRUVIC ACID × 2 NA SODIUM ION × 7 DTL L-TREITOL × 4 PG4 TETRAETHYLENE GLYCOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.30
Resolution 2.30 Å R-free 0.234
1QHM ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN Deposited 1999-05-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–625（624 aa） Fragment：RESIDUES 1-624
Chain B 2–625（624 aa） Fragment：RESIDUES 1-624
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；18% PEG-1000, 0.1 M HEPES/HCL PH7.6, VAPOUR DIFFUSION
Resolution 2.80 Å R-free 0.253
2PFL CRYSTAL STRUCTURE OF PFL FROM E.COLI Deposited 1999-05-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–760（759 aa）
Chain B 2–760（759 aa）
Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.3
Resolution 2.90 Å R-free 0.242
3PFL CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE Deposited 1999-05-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–759（759 aa）
Chain B 1–759（759 aa）
Not recorded OXM OXAMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.3
Resolution 2.60 Å R-free 0.251

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PFLB_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–759； UniProt 1–759 Author chain B； PDBConstruct 1–759； UniProt 1–759

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1mzo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1mzo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1mzo
Deposition date deposition_date2002-10-09
Structure title titleCrystal structure of pyruvate formate-lyase with pyruvate
Keywords keywordsENZYME-SUBSTRATE COMPLEX, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.79 Å
Radius of gyration Rg (electron density) rg_electron37.42 Å
Forward intensity I(0) i0435227000.00
Molecular weight molecular_weight170100.0 kDa
Excluded volume excluded_volume212500 ų
Envelope volume envelope_volume247510 ų
Hydration-shell volume shell_volume54582 ų
Envelope diameter envelope_diameter136.9 Å
Shell Rg shell_rg44.09 Å
Envelope Rg envelope_rg37.48 Å
Shape Rg shape_rg37.42 Å
Total Rg total_rg37.77 Å
Total atoms total_atoms11952
Residues n_residues1512
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax122.8 Å
Rg (real space) rg_real37.84 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real4.3520e+08
I(0) uncertainty (real space) i0_real_error7.0250e+06
Rg (reciprocal space) rg_reciprocal37.81 Å
I(0) (reciprocal space) i0_reciprocal435200000.0000
Solution quality estimate total_estimate0.8874
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.0 Å
Skewness Skewness skewness0.331
Kurtosis Kurtosis kurtosis-0.617
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha150200000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.900
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1mzoa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamilyc.7.1 — PFL-like glycyl radical enzymes
Family Family familyc.7.1.1 — PFL-like
Domain ID domain_idd1mzob_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamilyc.7.1 — PFL-like glycyl radical enzymes
Family Family familyc.7.1.1 — PFL-like

CATH v4.4 (2 domains)

Domain ID domain_id1mzoA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1mzoB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)