SAXSdb — 5lxf

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

Macrophage colony-stimulating factor 1

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 33–190 Chain B； UniProt 33–190	Mutation：C31S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；0.03M Bis-Tris pH 6.5; 0.17M Mg Formate; 16.67% PEG 3350; 0.07M Bis-Tris pH 5.5	Resolution 2.00 Å R-free 0.253

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 5LXF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HMC THREE-DIMENSIONAL STRUCTURE OF DIMERIC HUMAN RECOMBINANT MACROPHAGE COLONY STIMULATING FACTOR Deposited 1993-12-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–181（146 aa） Chain B 36–181（146 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
3UEZ Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine in complex with the viral receptor BARF1 Deposited 2011-10-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain F 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris HCl, 1.0M ammonium sulphate, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.41 Å R-free 0.274
3UEZ Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine in complex with the viral receptor BARF1 Deposited 2011-10-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain H 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris HCl, 1.0M ammonium sulphate, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.41 Å R-free 0.274
3UF2 Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine Deposited 2011-10-31	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain B 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.75 Å R-free 0.190
3UF2 Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine Deposited 2011-10-31	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain D 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.75 Å R-free 0.190
3UF2 Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine Deposited 2011-10-31	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain F 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.75 Å R-free 0.190
3UF2 Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine Deposited 2011-10-31	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain H 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.75 Å R-free 0.190
3UF2 Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine Deposited 2011-10-31	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain J 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.75 Å R-free 0.190
4ADF CRYSTAL STRUCTURE OF THE HUMAN COLONY-STIMULATING FACTOR 1 (hCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1 Deposited 2011-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain H 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain I 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain J 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain K 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain L 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS HCL, PH 8.50, 1.0 M AMMONIUM PHOSPHATE MONOBASIC	Resolution 4.40 Å R-free 0.276
4ADF CRYSTAL STRUCTURE OF THE HUMAN COLONY-STIMULATING FACTOR 1 (hCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1 Deposited 2011-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain S 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain T 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain U 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain V 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain W 33–181（149 aa） Fragment：UNP RESIDUES 33-181 Chain X 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS HCL, PH 8.50, 1.0 M AMMONIUM PHOSPHATE MONOBASIC	Resolution 4.40 Å R-free 0.276
4FA8 Multi-pronged modulation of cytokine signaling Deposited 2012-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 36–180（145 aa） Fragment：UNP residues 36-180 Chain F 36–180（145 aa） Fragment：UNP residues 36-180 Chain G 36–180（145 aa） Fragment：UNP residues 36-180	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8% PEG8000, 0.1M imidazole pH8.0, 0.22M calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.260
4FA8 Multi-pronged modulation of cytokine signaling Deposited 2012-05-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 36–180（145 aa） Fragment：UNP residues 36-180	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8% PEG8000, 0.1M imidazole pH8.0, 0.22M calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.260
4FA8 Multi-pronged modulation of cytokine signaling Deposited 2012-05-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain F 36–180（145 aa） Fragment：UNP residues 36-180 Chain G 36–180（145 aa） Fragment：UNP residues 36-180	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；8% PEG8000, 0.1M imidazole pH8.0, 0.22M calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.260
4WRL Structure of the human CSF-1:CSF-1R complex Deposited 2014-10-24	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 33–181（149 aa） Fragment：UNP residues 33-181 Chain D 33–181（149 aa） Fragment：UNP residues 33-181	Not recorded	SIA N-acetyl-alpha-neuraminic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5 and 28% w/v PEG 3350	Resolution 2.80 Å R-free 0.261
4WRM Structure of the human CSF-1:CSF-1R complex Deposited 2014-10-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 33–181（149 aa） Fragment：UNP RESIDUES 33-181	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M NaCl, 0.1 M Tris pH 8.0 and 8% w/v PEG 20000	Resolution 6.85 Å R-free 0.359

7 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSF1_HUMAN
Isoform	P09603-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–170； UniProt 33–190 Author chain B； PDBConstruct 13–170； UniProt 33–190

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	5lxf
Deposition date deposition_date	2016-09-21
Structure title title	Crystal structure of the human Macrophage Colony Stimulating Factor M- CSF_C31S variant
Keywords keywords	Drug design, rational protein engineering, receptor tyrosine kinase, osteoporosis, signaling protein; SIGNALING PROTEIN
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	25.59 Å
Radius of gyration Rg (electron density) rg_electron	24.90 Å
Forward intensity I(0) i0	21311300.00
Molecular weight molecular_weight	34375.0 kDa
Excluded volume excluded_volume	42726 Å³
Envelope volume envelope_volume	52175 Å³
Hydration-shell volume shell_volume	19328 Å³
Envelope diameter envelope_diameter	86.7 Å
Shell Rg shell_rg	29.73 Å
Envelope Rg envelope_rg	25.12 Å
Shape Rg shape_rg	24.91 Å
Total Rg total_rg	25.50 Å
Total atoms total_atoms	2407
Residues n_residues	295
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	85.0 Å
Rg (real space) rg_real	25.86 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.1310e+07
I(0) uncertainty (real space) i0_real_error	3.1860e+05
Rg (reciprocal space) rg_reciprocal	25.77 Å
I(0) (reciprocal space) i0_reciprocal	21310000.0000
Solution quality estimate total_estimate	0.8363
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.555
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2883000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.718; Smooth: 0.913

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5lxfa_
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	d5lxfb_
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	5lxfA00
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	5lxfB00
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	33.271 Å
Unit-cell length b length_b	65.471 Å
Unit-cell length c length_c	158.632 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	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	39.660 Å
R factor r_factor	0.1917
R_work r_work	0.1885
R_free r_free	0.2531

Description description	Macrophage colony-stimulating factor 1
Molecular weight formula_weight	21354.7 kDa
Mutation mutation	C31S
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2700

Crystal structure of the human Macrophage Colony Stimulating Factor M- CSF_C31S variant

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

Macrophage colony-stimulating factor 1

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 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	Komagataella phaffii GS115

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	261

fit	/app/data/saxs_computation/lx/5lxf/5lxf.fit
pddf	/app/data/pr_computation/lx/5lxf/5lxf.pr.out
profile	/app/data/saxs_computation/lx/5lxf/5lxf.dat