SAXSdb — 1hjf

▼

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–311	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

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 1HJF	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 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）	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 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–306（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 mutation/modification Different oligomeric state 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
1HJG Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258 Deposited 2001-01-15	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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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 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）	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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）	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 1–311； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hjf
Deposition date deposition_date	2001-01-15
Structure title title	Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258
Keywords keywords	;OXIDOREDUCTASE, ALTERNATIVE 2-OXOACIDS, CEPHEM ANTIBIOTIC BIOSYNTHESIS, CHEMICAL COSUBSTRATE RESCUE, CO-SUBSTRATE SELECTIVITY, 2- OXOGLUTARATE-DEPENDENT OXYGENASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.87 Å
Radius of gyration Rg (electron density) rg_electron	18.49 Å
Forward intensity I(0) i0	17340400.00
Molecular weight molecular_weight	30660.0 kDa
Excluded volume excluded_volume	38043 Å³
Envelope volume envelope_volume	44481 Å³
Hydration-shell volume shell_volume	19945 Å³
Envelope diameter envelope_diameter	64.1 Å
Shell Rg shell_rg	25.05 Å
Envelope Rg envelope_rg	18.79 Å
Shape Rg shape_rg	18.50 Å
Total Rg total_rg	19.40 Å
Total atoms total_atoms	2157
Residues n_residues	278
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

▼

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

Maximum dimension Dmax dmax	62.3 Å
Rg (real space) rg_real	19.76 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.7340e+07
I(0) uncertainty (real space) i0_real_error	2.1300e+05
Rg (reciprocal space) rg_reciprocal	19.77 Å
I(0) (reciprocal space) i0_reciprocal	17340000.0000
Solution quality estimate total_estimate	0.8191
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5056000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DEACETOXYCEPHALOSPORIN C SYNTHASE
Molecular weight formula_weight	34562.6 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2256

MDTTVPTFSLAELQQGLHQDEFRRCLRDKGLFYLTDCGLTDTELKSAKDIVIDFFEHGSEAEKRAVTSPVPTMRRGFTGLESESTAQITNTGSYSDYSMCYSMGTADNLFPSGDFERIWTQYFDRQYTASRAVAREVLRATGTEPDGGVEAFLDCEPLLRFRYFPQVPEHRSAEEQPLRMAPHYDLSMVTLIQQTPCANGFVSLQAEVGGAFTDLPYRPDAVLVFCGAIATLVTGGQVKAPRHHVAAPRRDQIAGSSQTSSVFFLRPNADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVNIRRTSKA

来源 Source

来源生物 organism	STREPTOMYCES CLAVULIGERUS
NCBI Class编号 ncbi_taxonomy_id	1901
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-OXO-4-METHYLPENTANOIC ACID
Molecular weight formula_weight	130.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1hjfa_
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	1hjfA00
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

▶

8. Citations (2)

▶

Unit-cell length a length_a	106.933 Å
Unit-cell length b length_b	106.933 Å
Unit-cell length c length_c	70.819 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	19.380 Å
R factor r_factor	0.2410
R_work r_work	0.2410
R_free r_free	0.2690

fit	/app/data/saxs_computation/hj/1hjf/1hjf.fit
pddf	/app/data/pr_computation/hj/1hjf/1hjf.pr.out
profile	/app/data/saxs_computation/hj/1hjf/1hjf.dat

Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258

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