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1amj

STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM

Method: X-RAY DIFFRACTION Dmax: 82.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ACONITASE

Bos taurus

UniProt P20004

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 28–780 Not recorded OH HYDROXIDE ION × 1 SO4 SULFATE ION × 1 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 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 1AMJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ACO CRYSTAL STRUCTURE OF ACONITASE WITH TRANSACONITATE BOUND Deposited 1993-01-17 Different construct Different mutation/modification 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) TRA ACONITATE ION × 1 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.05 Å
1AMI STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM Deposited 1994-11-11 Different ligand/ion Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–780（753 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 MIC ALPHA-METHYLISOCITRIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1C96 S642A:CITRATE COMPLEX OF ACONITASE Deposited 1999-07-31 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 29–782（754 aa）
Mutation：SER642ALA FLC CITRATE ANION × 1 SF4 IRON/SULFUR CLUSTER × 1 O OXYGEN ATOM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；2.6 M AMMONIUM SULFATE 0.35 M SODIUM CHLORIDE 0.25 M BIS-TRIS, pH 7.0, VAPOR DIFFUSION, temperature 295K
Resolution 1.81 Å
1C97 S642A:ISOCITRATE COMPLEX OF ACONITASE Deposited 1999-07-31 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 29–782（754 aa）
Mutation：SER642ALA SF4 IRON/SULFUR CLUSTER × 1 O OXYGEN ATOM × 1 ICT ISOCITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；2.6 M AMMONIUM SULFATE 0.35 M SODIUM CHLORIDE 0.25 M BIS-TRIS, pH 7.0, VAPOR DIFFUSION, temperature 295.K
Resolution 1.98 Å
1FGH COMPLEX WITH 4-HYDROXY-TRANS-ACONITATE Deposited 1996-09-14 Different construct Different mutation/modification 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 ATH 4-HYDROXY-ACONITATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.05 Å
1NIS CRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITRATE BOUND Deposited 1993-01-17 Different construct Different mutation/modification 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 NTC 2-HYDROXY-2-NITROMETHYL SUCCINIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.05 Å
1NIT CRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITRATE BOUND Deposited 1993-01-17 Different construct Different mutation/modification 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 SF4 IRON/SULFUR CLUSTER × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.05 Å
8ACN CRYSTAL STRUCTURES OF ACONITASE WITH ISOCITRATE AND NITROISOCITRATE BOUND Deposited 1991-05-15 Different construct Different mutation/modification Different ligand/ion Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–780（752 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SF4 IRON/SULFUR CLUSTER × 1 NIC NITROISOCITRIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACON_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–754； UniProt 28–780

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 1amj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1amj
Deposition date deposition_date1994-11-11
Structure title titleSTERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM
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_guinier26.39 Å
Radius of gyration Rg (electron density) rg_electron25.54 Å
Forward intensity I(0) i0113475000.00
Molecular weight molecular_weight82989.0 kDa
Excluded volume excluded_volume103450 ų
Envelope volume envelope_volume118180 ų
Hydration-shell volume shell_volume36991 ų
Envelope diameter envelope_diameter87.2 Å
Shell Rg shell_rg34.14 Å
Envelope Rg envelope_rg25.76 Å
Shape Rg shape_rg25.58 Å
Total Rg total_rg26.22 Å
Total atoms total_atoms5827
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 dmax82.2 Å
Rg (real space) rg_real26.25 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real1.1350e+08
I(0) uncertainty (real space) i0_real_error1.6110e+06
Rg (reciprocal space) rg_reciprocal26.30 Å
I(0) (reciprocal space) i0_reciprocal113500000.0000
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_primary31.5 Å
Skewness Skewness skewness0.212
Kurtosis Kurtosis kurtosis-0.421
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37370000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.979
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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_idd1amja1
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_idd1amja2
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_id1amjA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology499 — Aconitase; domain 3
Homologous superfamily homologous superfamily10 — Aconitase, domain 3
Domain ID domain_id1amjA02
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_id1amjA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology499 — Aconitase; domain 3
Homologous superfamily homologous superfamily10 — Aconitase, domain 3
Domain ID domain_id1amjA04
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 (6)

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9. Files and Curves (10)