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1dp2

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE

Method: X-RAY DIFFRACTION Dmax: 65.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RHODANESE

OrganismNot specified

UniProt P00586

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 1–293 Non-standard monomer：Yes (specific site not provided by mmCIF) LPB 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Crystals were obtained from ammonium sulfate. After soaking with 28% PEG 6000, 40 mM phosphate buffer, pH=7, 4 mM DL-lipoate was added , VAPOR DIFFUSION, SITTING DROP, temperature 20K, temperature 293K Resolution 2.01 Å R-free 0.230

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 1DP2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BOH SULFUR-SUBSTITUTED RHODANESE (ORTHORHOMBIC FORM) Deposited 1998-08-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–296（296 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.3
Resolution 2.30 Å R-free 0.215
1BOI N-TERMINALLY TRUNCATED RHODANESE Deposited 1998-08-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–296（296 aa） Fragment：DEL(1-7)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；pH 7.3
Resolution 2.20 Å R-free 0.219
1ORB ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED FORMS OF RHODANESE Deposited 1995-07-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–296（296 aa）
Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1RHD STRUCTURE OF BOVINE LIVER RHODANESE. I. STRUCTURE DETERMINATION AT 2.5 ANGSTROMS RESOLUTION AND A COMPARISON OF THE CONFORMATION AND SEQUENCE OF ITS TWO DOMAINS Deposited 1977-11-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–293（293 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1RHS SULFUR-SUBSTITUTED RHODANESE Deposited 1997-07-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–296（296 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 1.36 Å R-free 0.229
2ORA RHODANESE (THIOSULFATE: CYANIDE SULFURTRANSFERASE) Deposited 1996-02-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–296（296 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.99 Å
8Q5Z Crystal structure of bovine Thiosulfate sulfurtransferase Deposited 2023-08-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–297（297 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 6000, Tris, calcium chloride dihydrate
Resolution 1.50 Å R-free 0.163

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THTR_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–293； UniProt 1–293

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 1dp2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dp2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dp2
Deposition date deposition_date1999-12-23
Structure title titleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RHODANESE AND LIPOATE
Keywords keywordsRhodanese, liopate, sulfurtransferase, TRANSFERASE; TRANSFERASE
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_guinier19.68 Å
Radius of gyration Rg (electron density) rg_electron18.57 Å
Forward intensity I(0) i018972000.00
Molecular weight molecular_weight33146.0 kDa
Excluded volume excluded_volume41476 ų
Envelope volume envelope_volume46391 ų
Hydration-shell volume shell_volume20529 ų
Envelope diameter envelope_diameter64.5 Å
Shell Rg shell_rg25.26 Å
Envelope Rg envelope_rg18.88 Å
Shape Rg shape_rg18.57 Å
Total Rg total_rg19.50 Å
Total atoms total_atoms2339
Residues n_residues292
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 dmax65.0 Å
Rg (real space) rg_real19.57 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real1.8970e+07
I(0) uncertainty (real space) i0_real_error2.1910e+05
Rg (reciprocal space) rg_reciprocal19.58 Å
I(0) (reciprocal space) i0_reciprocal18970000.0000
Solution quality estimate total_estimate0.8785
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7 Å
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.329
Angular range angular_range— – 0.4050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5192000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dp2a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.46 — Rhodanese/Cell cycle control phosphatase
Superfamily Superfamily superfamilyc.46.1 — Rhodanese/Cell cycle control phosphatase
Family Family familyc.46.1.2 — Multidomain sulfurtransferase (rhodanese)
Domain ID domain_idd1dp2a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.46 — Rhodanese/Cell cycle control phosphatase
Superfamily Superfamily superfamilyc.46.1 — Rhodanese/Cell cycle control phosphatase
Family Family familyc.46.1.2 — Multidomain sulfurtransferase (rhodanese)

CATH v4.4 (2 domains)

Domain ID domain_id1dp2A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily10 — Rhodanese-like domain
Domain ID domain_id1dp2A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily10 — Rhodanese-like domain
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8. Citations (3)

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9. Files and Curves (10)