SAXSdb — 5d22

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

Granulocyte-macrophage colony-stimulating factor

Ovis aries

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 18–144	Not recorded	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M sodium acetate trihydrate 0.1 M TRIS hydrochloride pH 8.5 30% w/v PEG 4000	Resolution 1.99 Å R-free 0.229
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 18–144	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M sodium acetate trihydrate 0.1 M TRIS hydrochloride pH 8.5 30% w/v PEG 4000	Resolution 1.99 Å R-free 0.229

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 5D22	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5D28 Complex of GM-CSF/IL-2 inhibition factor with Granulocyte-macrophage colony-stimulating factor Deposited 2015-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 18–144（127 aa） Chain C 18–144（127 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.15 M ammonium sulfate, 0.1 M MES pH 6.0, 24 % PEG 4000	Resolution 2.85 Å R-free 0.235

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSF2_SHEEP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–127； UniProt 18–144 Author chain B； PDBConstruct 1–127； UniProt 18–144

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	5d22
Deposition date deposition_date	2015-08-05
Structure title title	Structure of ovine granulocyte-macrophage colony-stimulating factor
Keywords keywords	Signaling Protein, recombinant proteins, cytokine immunology, cytokine; CYTOKINE
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	21.30 Å
Radius of gyration Rg (electron density) rg_electron	20.32 Å
Forward intensity I(0) i0	13282800.00
Molecular weight molecular_weight	27376.0 kDa
Excluded volume excluded_volume	34214 Å³
Envelope volume envelope_volume	43129 Å³
Hydration-shell volume shell_volume	17987 Å³
Envelope diameter envelope_diameter	71.4 Å
Shell Rg shell_rg	26.43 Å
Envelope Rg envelope_rg	20.73 Å
Shape Rg shape_rg	20.33 Å
Total Rg total_rg	21.16 Å
Total atoms total_atoms	1917
Residues n_residues	241
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	70.8 Å
Rg (real space) rg_real	21.28 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.3280e+07
I(0) uncertainty (real space) i0_real_error	1.6640e+05
Rg (reciprocal space) rg_reciprocal	21.29 Å
I(0) (reciprocal space) i0_reciprocal	13280000.0000
Solution quality estimate total_estimate	0.8907
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.7 Å
Skewness Skewness skewness	0.278
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2349000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.947

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Granulocyte-macrophage colony-stimulating factor
Molecular weight formula_weight	14426.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2055

APTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVVSEMFDSQEPTCLQTRLELYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITFKSFKENLKDFLFIIPFDCWEPVQK

来源 Source

来源生物 organism	Ovis aries
通用名 common_name	Sheep
NCBI Class编号 ncbi_taxonomy_id	9940
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	121

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5d22a_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

Domain ID domain_id	d5d22b_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.2 — Short-chain cytokines

CATH v4.4 (2 domains)

Domain ID domain_id	5d22A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5d22B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	41.100 Å
Unit-cell length b length_b	77.020 Å
Unit-cell length c length_c	47.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.994 Å
Low-resolution limit resolution_low	38.510 Å
R factor r_factor	0.1900
R_work r_work	0.1881
R_free r_free	0.2286

fit	/app/data/saxs_computation/d2/5d22/5d22.fit
pddf	/app/data/pr_computation/d2/5d22/5d22.pr.out
profile	/app/data/saxs_computation/d2/5d22/5d22.dat

Structure of ovine granulocyte-macrophage colony-stimulating factor

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

Granulocyte-macrophage colony-stimulating factor

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