SAXSdb — 2rds

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

1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase

Streptomyces avermitilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 MAGNESIUM ION × 2 N-OXALYLGLYCINE × 1 (1S,3aS,5aR,8aS)-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylic acid × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q82IZ1_STRAW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–288； UniProt 1–285

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	2rds
Deposition date deposition_date	2007-09-24
Structure title title	Crystal Structure of PtlH with Fe/oxalylglycine and ent-1-deoxypentalenic acid bound
Keywords keywords	double stranded barrel helix, dioxygenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2rds__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2rds__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rds__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.73 Å
Rg (electron density)	17.45 Å
Total Rg	18.44 Å
Atom count	2133
Residues	261
Excluded volume	37528 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rds__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase
Molecular weight formula_weight	32588.6 kDa
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	2588

GSHMTNVTGDYTDCTPLLGDRAALDSFYEEHGYLFLRNVLDRDLVKTVAEQMREGLVALGAADPHATLEELTIDSFESVDEVAMHDYVKYDAFWNNPSTIKVFEQVFGEPVFVFLSTTIRYYPSQAGSEEPSFHYLTPFHQDGFYIGPNQDFRTFWIPLIRTTRESGGVALADGSHRRGKRDHVLNESFRRFGHPVRGIPPTEVSEDEHLLHSPMEPGDILLFHAHMCHKSIPNLSKDPRLMRMSMDTRVQPAKSHRGFNAMTPWTESAKDASKGIMAKITGTPTDVE

Source Source

Source organism organism	Streptomyces avermitilis
NCBI taxonomy ID ncbi_taxonomy_id	33903
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FE (III) 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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	N-OXALYLGLYCINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(1S,3aS,5aR,8aS)-1,7,7-trimethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene-4-carboxylic acid
Molecular weight formula_weight	234.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	409

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2rdsA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	620 — q2cbj1_9rhob like domain

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Unit-cell length a length_a	69.951 Å
Unit-cell length b length_b	89.387 Å
Unit-cell length c length_c	48.770 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1830
R_work r_work	0.1820
R_free r_free	0.2090

Crystal Structure of PtlH with Fe/oxalylglycine and ent-1-deoxypentalenic acid bound

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

1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2rds__assembly_1__model_1

2rds__assembly_1__model_1 | I(q)

2rds__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of PtlH with Fe/oxalylglycine and ent-1-deoxypentalenic acid bound

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

1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2rds__assembly_1__model_1

2rds__assembly_1__model_1 | I(q)

2rds__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)