2scu

A detailed description of the structure of Succinyl-COA synthetase from Escherichia coli

Method: X-RAY DIFFRACTION Dmax: 117.5 Å Quality: GOOD

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

PROTEIN (SUCCINYL-COA LIGASE)

Escherichia coli

UniProt P07459

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–289 Non-standard monomer:Yes (specific site not provided by mmCIF) PROTEIN (SUCCINYL-COA LIGASE) × 2 (P07460) COA COENZYME A × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.2;pH 7.2 Resolution 2.30 Å
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 2–289 Non-standard monomer:Yes (specific site not provided by mmCIF) PROTEIN (SUCCINYL-COA LIGASE) × 2 (P07460) COA COENZYME A × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.2;pH 7.2 Resolution 2.30 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.

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

View Construct and Data Evidence
UniProt name SUCD_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–288; UniProt 2–289 Author chain D; PDBConstruct 1–288; UniProt 2–289

PROTEIN (SUCCINYL-COA LIGASE)

Escherichia coli

UniProt P07460

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–388 Not recorded PROTEIN (SUCCINYL-COA LIGASE) × 2 (P07459) COA COENZYME A × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.2;pH 7.2 Resolution 2.30 Å
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–388 Not recorded PROTEIN (SUCCINYL-COA LIGASE) × 2 (P07459) COA COENZYME A × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.2;pH 7.2 Resolution 2.30 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.

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

View Construct and Data Evidence
UniProt name SUCC_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–388; UniProt 1–388 Author chain E; PDBConstruct 1–388; UniProt 1–388

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 2scu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2scu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2scu
Deposition date deposition_date1998-09-24
Structure title titleA detailed description of the structure of Succinyl-COA synthetase from Escherichia coli
Keywords keywordsCITRIC ACID CYCLE, HETEROTETRAMER, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.88
Radius of gyration Rg (electron density) rg_electron35.71
Forward intensity I(0) i0309083000.00
Molecular weight molecular_weight142770.0 kDa
Excluded volume excluded_volume179200 ų
Envelope volume envelope_volume223290 ų
Hydration-shell volume shell_volume52072 ų
Envelope diameter envelope_diameter119.6
Shell Rg shell_rg42.27
Envelope Rg envelope_rg35.04
Shape Rg shape_rg35.71
Total Rg total_rg36.13
Total atoms total_atoms10006
Residues n_residues1340
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax117.5
Rg (real space) rg_real35.88
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real3.0910e+08
I(0) uncertainty (real space) i0_real_error5.1890e+06
Rg (reciprocal space) rg_reciprocal35.88
I(0) (reciprocal space) i0_reciprocal309100000.0000
Solution quality estimate total_estimate0.8851
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.0
Skewness Skewness skewness0.351
Kurtosis Kurtosis kurtosis-0.403
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha72750000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.847

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2scua1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.8 — CoA-binding domain
Domain ID domain_idd2scua2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.4 — Succinyl-CoA synthetase domains
Family Family familyc.23.4.1 — Succinyl-CoA synthetase domains
Domain ID domain_idd2scub1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.4 — Succinyl-CoA synthetase domains
Family Family familyc.23.4.1 — Succinyl-CoA synthetase domains
Domain ID domain_idd2scub2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.4 — Succinyl-CoA synthetase, beta-chain, N-terminal domain
Domain ID domain_idd2scud1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.8 — CoA-binding domain
Domain ID domain_idd2scud2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.4 — Succinyl-CoA synthetase domains
Family Family familyc.23.4.1 — Succinyl-CoA synthetase domains
Domain ID domain_idd2scue1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.4 — Succinyl-CoA synthetase domains
Family Family familyc.23.4.1 — Succinyl-CoA synthetase domains
Domain ID domain_idd2scue2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.4 — Succinyl-CoA synthetase, beta-chain, N-terminal domain

CATH v4.4 (10 domains)

Domain ID domain_id2scuA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2scuA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily261 — Succinyl-CoA synthetase domains
Domain ID domain_id2scuB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
Domain ID domain_id2scuB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
Domain ID domain_id2scuB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily261 — Succinyl-CoA synthetase domains
Domain ID domain_id2scuD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2scuD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily261 — Succinyl-CoA synthetase domains
Domain ID domain_id2scuE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
Domain ID domain_id2scuE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
Domain ID domain_id2scuE03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily261 — Succinyl-CoA synthetase domains

8. Citations (4)

9. Files and Curves (10)