SAXSdb — 1dgp

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

ARISTOLOCHENE SYNTHASE

Penicillium roqueforti

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 40–339	Not recorded	FOF (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol × 1 FOH (2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；4% PEG 6000, 0.5M NACL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.264
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 40–339	Not recorded	FOF (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol × 1 FOH (2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；4% PEG 6000, 0.5M NACL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.264

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 1DGP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DI1 CRYSTAL STRUCTURE OF ARISTOLOCHENE SYNTHASE FROM PENICILLIUM ROQUEFORTI Deposited 1999-11-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–339（300 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.5M NACL, 4% PEG6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.273
1DI1 CRYSTAL STRUCTURE OF ARISTOLOCHENE SYNTHASE FROM PENICILLIUM ROQUEFORTI Deposited 1999-11-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 40–339（300 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.5M NACL, 4% PEG6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.273

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARIS_PENRO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–300； UniProt 40–339 Author chain B； PDBConstruct 1–300； UniProt 40–339

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	1dgp
Deposition date deposition_date	1999-11-24
Structure title title	ARISTOLOCHENE SYNTHASE FARNESOL COMPLEX
Keywords keywords	SESQUITERPENE CYCLASE, ISOPRENOID BIOSYNTHESIS, LYASE; LYASE
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	37.50 Å
Radius of gyration Rg (electron density) rg_electron	37.49 Å
Forward intensity I(0) i0	67562500.00
Molecular weight molecular_weight	67145.0 kDa
Excluded volume excluded_volume	84288 Å³
Envelope volume envelope_volume	113510 Å³
Hydration-shell volume shell_volume	26140 Å³
Envelope diameter envelope_diameter	127.1 Å
Shell Rg shell_rg	41.72 Å
Envelope Rg envelope_rg	36.81 Å
Shape Rg shape_rg	37.44 Å
Total Rg total_rg	37.96 Å
Total atoms total_atoms	4724
Residues n_residues	580
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	124.6 Å
Rg (real space) rg_real	37.97 Å
Rg uncertainty (real space) rg_real_error	1.51 Å
I(0) (real space) i0_real	6.7560e+07
I(0) uncertainty (real space) i0_real_error	1.2270e+06
Rg (reciprocal space) rg_reciprocal	37.69 Å
I(0) (reciprocal space) i0_reciprocal	67540000.0000
Solution quality estimate total_estimate	0.7002
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.383
Kurtosis Kurtosis kurtosis	-0.962
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10690000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.277; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.418; Smooth: 0.851

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ARISTOLOCHENE SYNTHASE
Molecular weight formula_weight	34497.2 kDa
EC 编号 ec_number	4.1.99.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4956

TPPPTQWSYLCHPRVKEVQDEVDGYFLENWKFPSFKAVRTFLDAKFSEVTCLYFPLALDDRIHFACRLLTVLFLIDDVLEHMSFADGEAYNNRLIPISRGDVLPDRTKPEEFILYDLWESMRAHDAELANEVLEPTFVFMRAQTDRARLSIHELGHYLEYREKDVGKALLSALMRFSMGLRLSADELQDMKALEANCAKQLSVVNDIYSYDKEEEASRTGHKEGAFLCSAVKVLAEESKLGIPATKRVLWSMTREWETVHDEIVAEKIASPDGCSEAAKAYMKGLEYQMSGNEQWSKTTR

来源 Source

来源生物 organism	Penicillium roqueforti
NCBI Class编号 ncbi_taxonomy_id	5082
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
Molecular weight formula_weight	222.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
Molecular weight formula_weight	222.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	200

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dgpa_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.4 — Aristolochene/pentalenene synthase

Domain ID domain_id	d1dgpb_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.4 — Aristolochene/pentalenene synthase

CATH v4.4 (2 domains)

Domain ID domain_id	1dgpA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	1dgpB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

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8. Citations (1)

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Unit-cell length a length_a	208.200 Å
Unit-cell length b length_b	208.200 Å
Unit-cell length c length_c	139.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2350
R_work r_work	0.2340
R_free r_free	0.2640

fit	/app/data/saxs_computation/dg/1dgp/1dgp.fit
pddf	/app/data/pr_computation/dg/1dgp/1dgp.pr.out
profile	/app/data/saxs_computation/dg/1dgp/1dgp.dat

ARISTOLOCHENE SYNTHASE FARNESOL COMPLEX