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5uqs

Crystal structure of Citrate synthase from Sus scrofa

Method: X-RAY DIFFRACTION Dmax: 95.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Citrate synthase, mitochondrial

OrganismNot specified

UniProt P00889

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–464 Chain C； UniProt 1–464 Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；0.2 NaTartrate pH 7.85, 20% PEG3350 Resolution 1.60 Å R-free 0.178

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 5UQS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CTS CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF TWO DIFFERENT FORMS OF CITRATE SYNTHASE AT 2.7 AND 1.7 ANGSTROMS RESOLUTION Deposited 1984-01-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–464（437 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
2CTS CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF TWO DIFFERENT FORMS OF CITRATE SYNTHASE AT 2.7 AND 1.7 ANGSTROMS RESOLUTION Deposited 1984-01-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–464（437 aa）
Not recorded COA COENZYME A × 2 CIT CITRIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
3ENJ Structure of Pig Heart Citrate Synthase at 1.78 A resolution Deposited 2008-09-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–464（437 aa）
Not recorded CYS CYSTEINE × 2 CL CHLORIDE ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.2；295 K；25% PEG 3350 in H2O in the presence of cystamine HCl, aspartame, benzamidine HCl and Tris-HCl buffer, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.78 Å R-free 0.222
4CTS CRYSTAL STRUCTURE ANALYSIS AND MOLECULAR MODEL OF A COMPLEX OF CITRATE SYNTHASE WITH OXALOACETATE AND S-ACETONYL-COENZYME A Deposited 1984-01-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–464（437 aa）
Chain B 28–464（437 aa）
Not recorded OAA OXALOACETATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CISY_PIG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–464； UniProt 1–464 Author chain C； PDBConstruct 1–464； UniProt 1–464

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 5uqs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5uqs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5uqs
Deposition date deposition_date2017-02-08
Structure title titleCrystal structure of Citrate synthase from Sus scrofa
Keywords keywordsporcine citrate synthase, TRANSFERASE; TRANSFERASE
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_guinier28.75 Å
Radius of gyration Rg (electron density) rg_electron27.80 Å
Forward intensity I(0) i0145642000.00
Molecular weight molecular_weight97341.0 kDa
Excluded volume excluded_volume122470 ų
Envelope volume envelope_volume145260 ų
Hydration-shell volume shell_volume41871 ų
Envelope diameter envelope_diameter101.7 Å
Shell Rg shell_rg36.65 Å
Envelope Rg envelope_rg28.04 Å
Shape Rg shape_rg27.81 Å
Total Rg total_rg28.57 Å
Total atoms total_atoms6851
Residues n_residues868
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 dmax95.5 Å
Rg (real space) rg_real28.65 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real1.4560e+08
I(0) uncertainty (real space) i0_real_error2.1440e+06
Rg (reciprocal space) rg_reciprocal28.69 Å
I(0) (reciprocal space) i0_reciprocal145600000.0000
Solution quality estimate total_estimate0.8799
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.7 Å
Skewness Skewness skewness0.273
Kurtosis Kurtosis kurtosis-0.270
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37130000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.982
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5uqsa_
Class classa — All alpha proteins
Fold Fold folda.103 — Citrate synthase
Superfamily Superfamily superfamilya.103.1 — Citrate synthase
Family Family familya.103.1.1 — Citrate synthase
Domain ID domain_idd5uqsc_
Class classa — All alpha proteins
Fold Fold folda.103 — Citrate synthase
Superfamily Superfamily superfamilya.103.1 — Citrate synthase
Family Family familya.103.1.1 — Citrate synthase

CATH v4.4 (4 domains)

Domain ID domain_id5uqsA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily10 — Citrate Synthase, domain 1
Domain ID domain_id5uqsA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily10 — Cytochrome P450-Terp, domain 2
Domain ID domain_id5uqsC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily10 — Citrate Synthase, domain 1
Domain ID domain_id5uqsC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily10 — Cytochrome P450-Terp, domain 2
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8. Citations (1)

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9. Files and Curves (10)