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1e5i

DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE.

Method: X-RAY DIFFRACTION Dmax: 63.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DEACETOXYCEPHALOSPORIN C SYNTHASE

STREPTOMYCES CLAVULIGERUS

UniProt P18548

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–306 Fragment：RESIDUES 1-306 FE2 FE (II) ION × 3 AKG 2-OXOGLUTARIC ACID × 3 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；100 MM HEPES-NAOH, PH 7.0, 0.5 MM PB(OAC)2(OH2)2, 5 MM 2-OXOGLUTARATE, GLYCEROL 5-10% (W/V), 1.4-1.65 M AMMONIUM SULPHATE Resolution 2.10 Å R-free 0.242
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–306 Fragment：RESIDUES 1-306 FE2 FE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；100 MM HEPES-NAOH, PH 7.0, 0.5 MM PB(OAC)2(OH2)2, 5 MM 2-OXOGLUTARATE, GLYCEROL 5-10% (W/V), 1.4-1.65 M AMMONIUM SULPHATE Resolution 2.10 Å R-free 0.242

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 1E5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DCS DEACETOXYCEPHALOSPORIN C SYNTHASE FROM S. CLAVULIGERUS Deposited 1998-06-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.30 Å R-free 0.150
1E5H DELTA-R307A DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH SUCCINATE AND CARBON DIOXIDE Deposited 2000-07-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–308（308 aa）
Mutation：YES FE2 FE (II) ION × 3 SIN SUCCINIC ACID × 3 CO2 CARBON DIOXIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；100 MM HEPES-NAOH, PH 7.0, 0.5 MM PB(OAC)2(OH2)2, 5 MM NA2SUCCINATE, 5 MM NAHCO3, GLYCEROL 5-10% (W/V), 1.4-1.6 M AMMONIUM SULPHATE
Resolution 1.96 Å R-free 0.252
1HJF Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258 Deposited 2001-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Mutation：YES FE2 FE (II) ION × 3 COI 2-OXO-4-METHYLPENTANOIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；HANGING DROP AT 20 DEGREES C. 100 MM HEPES-NAOH, PH 7.0, 6% (W/V) GLYCEROL, 5 MM 2-OXO-4-METHYLPENTANOATE, 1.5-1.7 M AMMONIUM SULPHATE CRYSTALS SOAKED IN 5 MM IRON(II) SULPHATE IN MOTHER LIQUOR UNDER ANAEROBIC CONDITIONS BEFORE DATA COLLECTION.
Resolution 1.60 Å R-free 0.269
1HJG Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258 Deposited 2001-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Mutation：YES FE2 FE (II) ION × 3 KIV 3-METHYL-2-OXOBUTANOIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；HANGING DROP AT 20 DEGREES C. 100 MM HEPES-NAOH, PH 7.0, 3% (W/V) GLYCEROL, 5 MM 2-OXO-3-METHYLBUTANOATE, 1.5-1.7 M AMMONIUM SULPHATE. CRYSTALS SOAKED IN 5 MM IRON(II) SULPHATE IN MOTHER LIQUOR UNDER ANAEROBIC CONDITIONS BEFORE DATA COLLECTION.
Resolution 1.50 Å R-free 0.241
1RXF DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II) Deposited 1998-06-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded FE FE (III) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.50 Å R-free 0.142
1RXG DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II) AND 2-OXOGLUTARATE Deposited 1998-06-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded FE FE (III) ION × 3 SO4 SULFATE ION × 3 AKG 2-OXOGLUTARIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.50 Å R-free 0.156
1UNB Deacetoxycephalosporin C synthase complexed with 2-oxoglutarate and ampicillin Deposited 2003-09-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded FE2 FE (II) ION × 3 AKG 2-OXOGLUTARIC ACID × 3 PN1 (2S,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPESPH7.5, pH 7.50
Resolution 1.50 Å R-free 0.236
1UO9 Deacetoxycephalosporin C synthase complexed with succinate Deposited 2003-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded FE2 FE (II) ION × 3 SIN SUCCINIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPES PH7.0, pH 7.50
Resolution 1.50 Å R-free 0.189
1UOB Deacetoxycephalosporin C synthase complexed with 2-oxoglutarate and penicillin G Deposited 2003-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded FE2 FE (II) ION × 3 PNN PENICILLIN G × 3 AKG 2-OXOGLUTARIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPES PH7.5, pH 7.50
Resolution 1.70 Å R-free 0.236
1UOF Deacetoxycephalosporin C synthase complexed with Penicillin G Deposited 2003-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded FE2 FE (II) ION × 3 PNN PENICILLIN G × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPESPH7.5, pH 7.50
Resolution 1.60 Å R-free 0.231
1UOG Deacetoxycephalosporin C synthase complexed with deacetoxycephalosporin C Deposited 2003-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded P1C DEACETOXYCEPHALOSPORIN-C × 3 FE2 FE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPESPH7.5, pH 7.50
Resolution 1.70 Å R-free 0.242
1W28 Conformational flexibility of the C-terminus with implications for substrate binding and catalysis in a new crystal form of deacetoxycephalosporin C synthase Deposited 2004-06-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–311（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；100 MM HEPES-NAOH PH 8, 0.9-1.1 M AMSO4
Resolution 2.30 Å R-free 0.223
1W2A Deacetoxycephalosporin C synthase (with his-tag) complexed with Fe(II) and ethylene glycol Deposited 2004-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 1–311（311 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 FE FE (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；100 MM HEPES PH8, 0.9-1.1 M AMSO4, pH 8.00
Resolution 2.51 Å R-free 0.254
1W2N Deacetoxycephalosporin C synthase (with a N-terminal his-tag) in complex with Fe(II) and ampicillin Deposited 2004-07-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–311（311 aa）
Not recorded FE FE (III) ION × 1 PN1 (2S,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；100 MM HEPES, PH 8 AND 0.9-1.1M AMSO4
Resolution 2.70 Å R-free 0.287
1W2O Deacetoxycephalosporin C synthase (with a N-terminal his-tag) in complex with Fe(II) and deacetoxycephalosporin C Deposited 2004-07-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–311（311 aa）
Not recorded FE FE (III) ION × 1 P1C DEACETOXYCEPHALOSPORIN-C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；100 MM HEPES PH 8, 0.9-1.1 M AMSO4
Resolution 3.00 Å R-free 0.334
2JB8 Deacetoxycephalosporin C synthase complexed with 5-hydroxy-4-keto valeric acid Deposited 2006-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–311（311 aa）
Not recorded FE FE (III) ION × 3 HKV 4,5-DIOXOPENTANOIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.53 Å R-free 0.249

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CEFE_STRCL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–306； UniProt 1–306

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 1e5i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1e5i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1e5i
Deposition date deposition_date2000-07-26
Structure title titleDELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE.
Keywords keywordsFERROUS OXYGENASE, CEPHALOSPORIN, 2-OXOGLUTARATE, C-TERMINUS ANTIBIOTICS, OXIDOREDUCTASE, OXIDATIVE COUPLING CONTROL; OXIDOREDUCTASE
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_guinier19.40 Å
Radius of gyration Rg (electron density) rg_electron18.12 Å
Forward intensity I(0) i016133700.00
Molecular weight molecular_weight29705.0 kDa
Excluded volume excluded_volume36874 ų
Envelope volume envelope_volume41766 ų
Hydration-shell volume shell_volume19159 ų
Envelope diameter envelope_diameter62.1 Å
Shell Rg shell_rg24.53 Å
Envelope Rg envelope_rg18.45 Å
Shape Rg shape_rg18.13 Å
Total Rg total_rg18.99 Å
Total atoms total_atoms2088
Residues n_residues268
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 dmax63.0 Å
Rg (real space) rg_real19.30 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real1.6130e+07
I(0) uncertainty (real space) i0_real_error2.2720e+05
Rg (reciprocal space) rg_reciprocal19.32 Å
I(0) (reciprocal space) i0_reciprocal16130000.0000
Solution quality estimate total_estimate0.8092
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.0 Å
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.331
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4633000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1e5ia_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.2 — Clavaminate synthase-like
Family Family familyb.82.2.1 — Penicillin synthase-like

CATH v4.4 (1 domains)

Domain ID domain_id1e5iA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily330 — B-lactam Antibiotic, Isopenicillin N Synthase; Chain
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8. Citations (2)

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9. Files and Curves (10)