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1qhm

ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN

Method: X-RAY DIFFRACTION Dmax: 116.7 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 2–625 Chain B； UniProt 2–625 Fragment：RESIDUES 1-624 No other associated polymer 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

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 1QHM 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 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）
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 construct 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
1MZO Crystal structure of pyruvate formate-lyase with pyruvate Deposited 2002-10-09 Different construct 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 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
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 construct 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 1–624； UniProt 2–625 Author chain B； PDBConstruct 1–624； UniProt 2–625

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 1qhm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1qhm
Deposition date deposition_date1999-05-19
Structure title titleESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN
Keywords keywordsPYRUVATE FORMATE LYASE, ANAEROBIC, HOMODIMER, ENZYME MECHANISM, LYASE-TRANSFERASE COMPLEX; LYASE/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_guinier35.91 Å
Radius of gyration Rg (electron density) rg_electron35.40 Å
Forward intensity I(0) i0285363000.00
Molecular weight molecular_weight136220.0 kDa
Excluded volume excluded_volume170000 ų
Envelope volume envelope_volume209740 ų
Hydration-shell volume shell_volume49260 ų
Envelope diameter envelope_diameter120.0 Å
Shell Rg shell_rg41.84 Å
Envelope Rg envelope_rg35.70 Å
Shape Rg shape_rg35.43 Å
Total Rg total_rg35.70 Å
Total atoms total_atoms9576
Residues n_residues1224
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 dmax116.7 Å
Rg (real space) rg_real35.89 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real2.8540e+08
I(0) uncertainty (real space) i0_real_error4.6260e+06
Rg (reciprocal space) rg_reciprocal35.90 Å
I(0) (reciprocal space) i0_reciprocal285400000.0000
Solution quality estimate total_estimate0.8981
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.8 Å
Skewness Skewness skewness0.292
Kurtosis Kurtosis kurtosis-0.519
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha67910000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.922
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1qhma_
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_idd1qhmb_
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_id1qhmA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1qhmB00
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 (2)

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9. Files and Curves (10)