SAXSdb — 1a59

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

CITRATE SYNTHASE

Antarctic bacterium DS2-3R

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 2–379	Not recorded	COA COENZYME A × 2 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.09 Å R-free 0.236

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CISY_ABDS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–378； UniProt 2–379

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1a59
Deposition date deposition_date	1998-02-20
Structure title title	COLD-ACTIVE CITRATE SYNTHASE
Keywords keywords	COLD-ACTIVITY; COLD-ACTIVITY
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.23 Å
Radius of gyration Rg (electron density) rg_electron	21.14 Å
Forward intensity I(0) i0	31705900.00
Molecular weight molecular_weight	42028.0 kDa
Excluded volume excluded_volume	52060 Å³
Envelope volume envelope_volume	63851 Å³
Hydration-shell volume shell_volume	24593 Å³
Envelope diameter envelope_diameter	81.1 Å
Shell Rg shell_rg	28.41 Å
Envelope Rg envelope_rg	22.46 Å
Shape Rg shape_rg	21.14 Å
Total Rg total_rg	22.05 Å
Total atoms total_atoms	2951
Residues n_residues	377
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	78.5 Å
Rg (real space) rg_real	22.20 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	3.1710e+07
I(0) uncertainty (real space) i0_real_error	3.9420e+05
Rg (reciprocal space) rg_reciprocal	22.21 Å
I(0) (reciprocal space) i0_reciprocal	31710000.0000
Solution quality estimate total_estimate	0.8498
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.387
Kurtosis Kurtosis kurtosis	-0.020
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6750000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CITRATE SYNTHASE
Molecular weight formula_weight	41749.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2951

TEPTIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSELKAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKAMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGEEAAPEVVEAFNVSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGIRKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKHYDRPEMLGLYNGLEAAMEEAKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITGWTAHIMEQVADNALIRPLSEYNGPEQRQVP

来源 Source

来源生物 organism	Antarctic bacterium DS2-3R
NCBI Class编号 ncbi_taxonomy_id	56673
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a59a_
Class class	a — All alpha proteins
Fold Fold fold	a.103 — Citrate synthase
Superfamily Superfamily superfamily	a.103.1 — Citrate synthase
Family Family family	a.103.1.1 — Citrate synthase

CATH v4.4 (2 domains)

Domain ID domain_id	1a59A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Citrate Synthase, domain 1

Domain ID domain_id	1a59A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome P450-Terp, domain 2

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8. Citations (1)

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Unit-cell length a length_a	70.800 Å
Unit-cell length b length_b	70.800 Å
Unit-cell length c length_c	307.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	0.2360

fit	/app/data/saxs_computation/a5/1a59/1a59.fit
pddf	/app/data/pr_computation/a5/1a59/1a59.pr.out
profile	/app/data/saxs_computation/a5/1a59/1a59.dat

COLD-ACTIVE CITRATE SYNTHASE

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

CITRATE SYNTHASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction