1cqj

CRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE

Method: X-RAY DIFFRACTION Dmax: 116.8 Å Quality: GOOD

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

SUCCINYL-COA SYNTHETASE ALPHA CHAIN

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 2–287 Chain D; UniProt 2–287 Fragment:ALPHA SUBUNIT SUCCINYL-COA SYNTHETASE BETA CHAIN × 2 (P07460) PO4 PHOSPHATE ION × 4 COA COENZYME A × 3 X-RAY DIFFRACTION X-ray crystallization conditions:MICRODIALYSIS;pH 7.3;294 K;ammonium sulfate, potassium phosphate, coenzyme A, pH 7.3, MICRODIALYSIS, temperature 294K Resolution 2.90 Å R-free 0.228

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 8 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 1–286; UniProt 2–287 Author chain D; PDBConstruct 1–286; UniProt 2–287

SUCCINYL-COA SYNTHETASE BETA CHAIN

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 1–385 Chain E; UniProt 1–385 Fragment:BETA SUBUNIT SUCCINYL-COA SYNTHETASE ALPHA CHAIN × 2 (P07459) PO4 PHOSPHATE ION × 4 COA COENZYME A × 3 X-RAY DIFFRACTION X-ray crystallization conditions:MICRODIALYSIS;pH 7.3;294 K;ammonium sulfate, potassium phosphate, coenzyme A, pH 7.3, MICRODIALYSIS, temperature 294K Resolution 2.90 Å R-free 0.228

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 3 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 1–385; UniProt 1–385 Author chain E; PDBConstruct 1–385; UniProt 1–385

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 1cqj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cqj
Deposition date deposition_date1999-08-06
Structure title titleCRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE
Keywords keywordsATP-GRASP FOLD, ROSSMANN FOLD, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.93
Radius of gyration Rg (electron density) rg_electron35.76
Forward intensity I(0) i0310562000.00
Molecular weight molecular_weight143050.0 kDa
Excluded volume excluded_volume179510 ų
Envelope volume envelope_volume224030 ų
Hydration-shell volume shell_volume52148 ų
Envelope diameter envelope_diameter119.4
Shell Rg shell_rg42.42
Envelope Rg envelope_rg35.08
Shape Rg shape_rg35.76
Total Rg total_rg36.19
Total atoms total_atoms10025
Residues n_residues1342
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 dmax116.8
Rg (real space) rg_real35.93
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real3.1060e+08
I(0) uncertainty (real space) i0_real_error5.5380e+06
Rg (reciprocal space) rg_reciprocal35.93
I(0) (reciprocal space) i0_reciprocal310600000.0000
Solution quality estimate total_estimate0.8847
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.8
Skewness Skewness skewness0.350
Kurtosis Kurtosis kurtosis-0.408
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha74540000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.812

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_idd1cqja1
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_idd1cqja2
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_idd1cqjb1
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_idd1cqjb2
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_idd1cqjd1
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_idd1cqjd2
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_idd1cqje1
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_idd1cqje2
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_id1cqjA01
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_id1cqjA02
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_id1cqjB01
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_id1cqjB02
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_id1cqjB03
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_id1cqjD01
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_id1cqjD02
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_id1cqjE01
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_id1cqjE02
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_id1cqjE03
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)