1cqi

Crystal Structure of the Complex of ADP and MG2+ with Dephosphorylated E. Coli Succinyl-CoA Synthetase

Method: X-RAY DIFFRACTION Dmax: 119.2 Å Quality: GOOD

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

PROTEIN (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 PROTEIN (SUCCINYL-COA SYNTHETASE BETA CHAIN) × 2 (P07460) PO4 PHOSPHATE ION × 2 COA COENZYME A × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.3;AMMONIUM SULFATE, POTASSIUM PHOSPHATE, COENZYME A, pH 7.30, VAPOR DIFFUSION, HANGING DROP Resolution 3.30 Å R-free 0.247

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

PROTEIN (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 PROTEIN (SUCCINYL-COA SYNTHETASE ALPHA CHAIN) × 2 (P07459) PO4 PHOSPHATE ION × 2 COA COENZYME A × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.3;AMMONIUM SULFATE, POTASSIUM PHOSPHATE, COENZYME A, pH 7.30, VAPOR DIFFUSION, HANGING DROP Resolution 3.30 Å R-free 0.247

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 1cqi

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cqi
Deposition date deposition_date1999-08-06
Structure title titleCrystal Structure of the Complex of ADP and MG2+ with 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_guinier36.27
Radius of gyration Rg (electron density) rg_electron36.14
Forward intensity I(0) i0314899000.00
Molecular weight molecular_weight143500.0 kDa
Excluded volume excluded_volume179840 ų
Envelope volume envelope_volume232710 ų
Hydration-shell volume shell_volume53438 ų
Envelope diameter envelope_diameter121.8
Shell Rg shell_rg42.85
Envelope Rg envelope_rg35.54
Shape Rg shape_rg36.14
Total Rg total_rg36.55
Total atoms total_atoms10054
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 dmax119.2
Rg (real space) rg_real36.27
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real3.1490e+08
I(0) uncertainty (real space) i0_real_error5.7850e+06
Rg (reciprocal space) rg_reciprocal36.27
I(0) (reciprocal space) i0_reciprocal314900000.0000
Solution quality estimate total_estimate0.8842
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.6
Skewness Skewness skewness0.355
Kurtosis Kurtosis kurtosis-0.383
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85380000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.854

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1cqia1
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_idd1cqia2
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_idd1cqib1
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_idd1cqib2
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_idd1cqid1
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_idd1cqid2
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_idd1cqie1
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_idd1cqie2
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_id1cqiA01
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_id1cqiA02
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_id1cqiB01
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_id1cqiB02
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_id1cqiB03
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_id1cqiD01
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_id1cqiD02
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_id1cqiE01
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_id1cqiE02
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_id1cqiE03
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)