SAXSdb — 1w28

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DEACETOXYCEPHALOSPORIN C SYNTHASE

STREPTOMYCES CLAVULIGERUS

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–311	Not recorded	No other associated polymer	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

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 1W28	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 oligomeric state 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 oligomeric state 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
1E5I DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE. Deposited 2000-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–306（306 aa） Fragment：RESIDUES 1-306	Not recorded	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
1E5I DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE. Deposited 2000-07-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–306（306 aa） Fragment：RESIDUES 1-306	Not recorded	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
1HJF Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258 Deposited 2001-01-15	Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
1W2A Deacetoxycephalosporin C synthase (with his-tag) complexed with Fe(II) and ethylene glycol Deposited 2004-07-01	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 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 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 oligomeric state 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 17 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 21–331； UniProt 1–311

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1w28
Deposition date deposition_date	2004-06-30
Structure title title	Conformational flexibility of the C-terminus with implications for substrate binding and catalysis in a new crystal form of deacetoxycephalosporin C synthase
Keywords keywords	OXIDOREDUCTASE, CEPHALOSPORIN, PENICILLIN, MONONUCLEAR FERROUS ENZYMES, 2-OXOGLUTARATE DEPENDENT OXYGENASES; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.97 Å
Radius of gyration Rg (electron density) rg_electron	18.64 Å
Forward intensity I(0) i0	16219500.00
Molecular weight molecular_weight	29927.0 kDa
Excluded volume excluded_volume	37262 Å³
Envelope volume envelope_volume	44174 Å³
Hydration-shell volume shell_volume	19686 Å³
Envelope diameter envelope_diameter	62.9 Å
Shell Rg shell_rg	25.07 Å
Envelope Rg envelope_rg	18.90 Å
Shape Rg shape_rg	18.63 Å
Total Rg total_rg	19.60 Å
Total atoms total_atoms	2109
Residues n_residues	272
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	61.9 Å
Rg (real space) rg_real	19.85 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.6220e+07
I(0) uncertainty (real space) i0_real_error	1.9040e+05
Rg (reciprocal space) rg_reciprocal	19.87 Å
I(0) (reciprocal space) i0_reciprocal	16220000.0000
Solution quality estimate total_estimate	0.9037
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.170
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3810000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.994

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1w28a_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.1 — Penicillin synthase-like

CATH v4.4 (1 domains)

Domain ID domain_id	1w28A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	330 — B-lactam Antibiotic, Isopenicillin N Synthase; Chain

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8. Citations (1)

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Unit-cell length a length_a	138.000 Å
Unit-cell length b length_b	138.000 Å
Unit-cell length c length_c	48.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.180 Å
R factor r_factor	0.1980
R_work r_work	0.1970
R_free r_free	0.2230

Description description	DEACETOXYCEPHALOSPORIN C SYNTHASE
Molecular weight formula_weight	36763.0 kDa
EC 编号 ec_number	1.14.20.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2249

Conformational flexibility of the C-terminus with implications for substrate binding and catalysis in a new crystal form of deacetoxycephalosporin C synthase

1. Protein Identity and Related Structures Protein Identity & Related Structures

DEACETOXYCEPHALOSPORIN C SYNTHASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	STREPTOMYCES CLAVULIGERUS
NCBI Class编号 ncbi_taxonomy_id	1901
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	140

fit	/app/data/saxs_computation/w2/1w28/1w28.fit
pddf	/app/data/pr_computation/w2/1w28/1w28.pr.out
profile	/app/data/saxs_computation/w2/1w28/1w28.dat