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6acn

STRUCTURE OF ACTIVATED ACONITASE. FORMATION OF THE (4FE-4S) CLUSTER IN THE CRYSTAL

Method: X-RAY DIFFRACTION Dmax: 83.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ACONITASE

Sus scrofa

UniProt P16276

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 29–781 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 SF4 IRON/SULFUR CLUSTER × 1 TRC TRICARBALLYLIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å

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 6ACN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B0J CRYSTAL STRUCTURE OF ACONITASE WITH ISOCITRATE Deposited 1998-11-10 Different mutation/modification Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–781（753 aa）
Mutation：S642A SF4 IRON/SULFUR CLUSTER × 1 ICT ISOCITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.50 Å
1B0K S642A:FLUOROCITRATE COMPLEX OF ACONITASE Deposited 1998-11-11 Different mutation/modification Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–781（753 aa）
Mutation：S642A FLC CITRATE ANION × 1 SF4 IRON/SULFUR CLUSTER × 1 O OXYGEN ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.50 Å
1B0M ACONITASE R644Q:FLUOROCITRATE COMPLEX Deposited 1998-11-11 Different mutation/modification Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–781（753 aa）
Mutation：R644Q FLC CITRATE ANION × 1 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.50 Å
5ACN STRUCTURE OF ACTIVATED ACONITASE. FORMATION OF THE (4FE-4S) CLUSTER IN THE CRYSTAL Deposited 1990-01-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–781（753 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 F3S FE3-S4 CLUSTER × 1 TRC TRICARBALLYLIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
7ACN CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRATE BOUND Deposited 1991-05-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–781（753 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 1 ICT ISOCITRIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACON_PIG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–754； UniProt 29–781

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 6acn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6acn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6acn
Deposition date deposition_date1990-01-16
Structure title titleSTRUCTURE OF ACTIVATED ACONITASE. FORMATION OF THE (4FE-4S) CLUSTER IN THE CRYSTAL
Keywords keywordsLYASE(CARBON-OXYGEN); LYASE(CARBON-OXYGEN)
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_guinier26.40 Å
Radius of gyration Rg (electron density) rg_electron25.56 Å
Forward intensity I(0) i0114418000.00
Molecular weight molecular_weight83299.0 kDa
Excluded volume excluded_volume103840 ų
Envelope volume envelope_volume118920 ų
Hydration-shell volume shell_volume37108 ų
Envelope diameter envelope_diameter87.3 Å
Shell Rg shell_rg34.26 Å
Envelope Rg envelope_rg25.87 Å
Shape Rg shape_rg25.60 Å
Total Rg total_rg26.26 Å
Total atoms total_atoms5848
Residues n_residues753
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 dmax83.3 Å
Rg (real space) rg_real26.27 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real1.1440e+08
I(0) uncertainty (real space) i0_real_error1.5680e+06
Rg (reciprocal space) rg_reciprocal26.31 Å
I(0) (reciprocal space) i0_reciprocal114400000.0000
Solution quality estimate total_estimate0.8979
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.9 Å
Skewness Skewness skewness0.214
Kurtosis Kurtosis kurtosis-0.417
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40530000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6acna1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamilyc.8.2 — LeuD/IlvD-like
Family Family familyc.8.2.1 — LeuD-like
Domain ID domain_idd6acna2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.83 — Aconitase iron-sulfur domain
Superfamily Superfamily superfamilyc.83.1 — Aconitase iron-sulfur domain
Family Family familyc.83.1.1 — Aconitase iron-sulfur domain

CATH v4.4 (4 domains)

Domain ID domain_id6acnA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology499 — Aconitase; domain 3
Homologous superfamily homologous superfamily10 — Aconitase, domain 3
Domain ID domain_id6acnA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1060 — Aconitase; Domain 2
Homologous superfamily homologous superfamily10 — Aconitase, Domain 2
Domain ID domain_id6acnA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology499 — Aconitase; domain 3
Homologous superfamily homologous superfamily10 — Aconitase, domain 3
Domain ID domain_id6acnA04
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology19 — Aconitase; domain 4
Homologous superfamily homologous superfamily10 — Aconitase, domain 4
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8. Citations (3)

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9. Files and Curves (10)