SAXSdb — 5zo6

▼

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

Granulocyte colony-stimulating factor

Homo sapiens

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 X； UniProt 37–205	Fragment：UNP residues 37-205 Mutation：C11S, A166G	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；sodium acetate trihydrate, sodium chloride dehydrate, PEG 1500, MPD	Resolution 1.70 Å R-free 0.217

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 5ZO6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CD9 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR Deposited 1999-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 13–186（174 aa） Chain C 13–186（174 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.80 Å R-free 0.319
1GNC STRUCTURE AND DYNAMICS OF THE HUMAN GRANULOCYTE COLONY-STIMULATING FACTOR DETERMINED BY NMR SPECTROSCOPY. LOOP MOBILITY IN A FOUR-HELIX-BUNDLE PROTEIN Deposited 1994-03-08	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–207（177 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1PGR 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR Deposited 1999-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 13–186（174 aa） Chain C 13–186（174 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 3.50 Å
1PGR 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR Deposited 1999-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 13–186（174 aa） Chain G 13–186（174 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 3.50 Å
1RHG THE STRUCTURE OF GRANULOCYTE-COLONY-STIMULATING FACTOR AND ITS RELATIONSHIP TO THOSE OF OTHER GROWTH FACTORS Deposited 1993-01-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 31–207（177 aa） Chain B 31–207（177 aa） Chain C 31–207（177 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
2D9Q Crystal Structure of the Human GCSF-Receptor Signaling Complex Deposited 2005-12-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 31–204（174 aa） Fragment：residues 1-174	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；0.2M ammonium phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.284
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 40–202（163 aa） Fragment：UNP residues 40-202 Chain C 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218
5GW9 Crystal structure of C163, a backbone circularized G-CSF Deposited 2016-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 40–202（163 aa） Fragment：UNP residues 40-202 Chain D 40–202（163 aa） Fragment：UNP residues 40-202	Mutation：P40S, C47S, A205G Mutation：P40S, C47S, A205G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.4M Ammonium sulfate	Resolution 1.65 Å R-free 0.218

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–166； UniProt 37–205

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5zo6
Deposition date deposition_date	2018-04-12
Structure title title	Crystal structure of C166, a backbone circularized G-CSF
Keywords keywords	cytokine, four-helix bundle, back-bone circularization; CYTOKINE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.59 Å
Radius of gyration Rg (electron density) rg_electron	16.60 Å
Forward intensity I(0) i0	5765240.00
Molecular weight molecular_weight	17859.0 kDa
Excluded volume excluded_volume	22575 Å³
Envelope volume envelope_volume	26777 Å³
Hydration-shell volume shell_volume	14025 Å³
Envelope diameter envelope_diameter	59.6 Å
Shell Rg shell_rg	21.79 Å
Envelope Rg envelope_rg	16.84 Å
Shape Rg shape_rg	16.56 Å
Total Rg total_rg	17.64 Å
Total atoms total_atoms	1256
Residues n_residues	166
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

▼

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

Maximum dimension Dmax dmax	57.0 Å
Rg (real space) rg_real	17.54 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	5.7650e+06
I(0) uncertainty (real space) i0_real_error	7.4190e+04
Rg (reciprocal space) rg_reciprocal	17.55 Å
I(0) (reciprocal space) i0_reciprocal	5765000.0000
Solution quality estimate total_estimate	0.7997
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.259
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1740000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5zo6x_
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.26.1.1 — Long-chain cytokines

CATH v4.4 (1 domains)

Domain ID domain_id	5zo6X00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	47.180 Å
Unit-cell length b length_b	48.050 Å
Unit-cell length c length_c	54.960 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	36.170 Å
R factor r_factor	0.1697
R_work r_work	0.1669
R_free r_free	0.2167

Description description	Granulocyte colony-stimulating factor
Molecular weight formula_weight	17893.6 kDa
Mutation mutation	C11S, A166G
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	1374

Crystal structure of C166, a backbone circularized G-CSF

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

Granulocyte 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

fit	/app/data/saxs_computation/zo/5zo6/5zo6.fit
pddf	/app/data/pr_computation/zo/5zo6/5zo6.pr.out
profile	/app/data/saxs_computation/zo/5zo6/5zo6.dat