SAXSdb — 1srs

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

PROTEIN (SERUM RESPONSE FACTOR (SRF))

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 87–178 Chain B； UniProt 87–178	Not recorded	;DNA (5'-D(CPCP(5IU)PTPCPCPTPAPAPTPTPAPGPGPCPCPAPTPG)-3') ; × 1 ;DNA (5'-D(CPCPAPTPGPGPCPCPTPAPAPTPTPAPGPGPA PAPG)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K	Resolution 3.20 Å

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 1SRS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 132–223（92 aa） Fragment：CORE RESIDUES 132-223 Chain B 132–223（92 aa） Fragment：CORE RESIDUES 132-223	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 132–223（92 aa） Fragment：CORE RESIDUES 132-223 Chain E 132–223（92 aa） Fragment：CORE RESIDUES 132-223	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285
1K6O Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex Deposited 2001-10-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 133–235（103 aa） Fragment：133-235 Chain C 133–235（103 aa） Fragment：133-235	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.19 Å R-free 0.276

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRF_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–92； UniProt 87–178 Author chain B； PDBConstruct 1–92； UniProt 87–178

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	1srs
Deposition date deposition_date	1995-07-28
Structure title title	SERUM RESPONSE FACTOR (SRF) CORE COMPLEXED WITH SPECIFIC SRE DNA
Keywords keywords	TRANSCRIPTION REGULATION, MADS-DOMAIN, COMPLEX (DNA BINDING PROTEIN-DNA), TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	20.44 Å
Radius of gyration Rg (electron density) rg_electron	19.35 Å
Forward intensity I(0) i0	23832800.00
Molecular weight molecular_weight	30365.0 kDa
Excluded volume excluded_volume	35023 Å³
Envelope volume envelope_volume	43219 Å³
Hydration-shell volume shell_volume	18909 Å³
Envelope diameter envelope_diameter	62.0 Å
Shell Rg shell_rg	25.33 Å
Envelope Rg envelope_rg	19.42 Å
Shape Rg shape_rg	19.30 Å
Total Rg total_rg	20.15 Å
Total atoms total_atoms	2074
Residues n_residues	201
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	61.3 Å
Rg (real space) rg_real	20.35 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	2.3830e+07
I(0) uncertainty (real space) i0_real_error	3.0710e+05
Rg (reciprocal space) rg_reciprocal	20.37 Å
I(0) (reciprocal space) i0_reciprocal	23830000.0000
Solution quality estimate total_estimate	0.9186
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.671
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2708000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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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	;DNA (5'-D(CPCP(5IU)PTPCPCPTPAPAPTPTPAPGPGPCPCPAPTP*G)-3') ;
Molecular weight formula_weight	5867.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	W
Atom count atom_count	2074

CCUTCCTAATTAGGCCATG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPCPAPTPGPGPCPCPTPAPAPTPTPAPGPGPA PAP*G)-3') ;
Molecular weight formula_weight	5853.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CCATGGCCTAATTAGGAAG

Entity 3 Entity 3 polymer

Description description	PROTEIN (SERUM RESPONSE FACTOR (SRF))
Molecular weight formula_weight	10300.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

SGAKPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQPMITSETGKALIQTCLNSPD

来源 Source

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 BL21(DE3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1srsa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

Domain ID domain_id	d1srsb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

CATH v4.4 (2 domains)

Domain ID domain_id	1srsA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

Domain ID domain_id	1srsB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

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8. Citations (1)

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Unit-cell length a length_a	106.840 Å
Unit-cell length b length_b	106.840 Å
Unit-cell length c length_c	76.880 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	—

fit	/app/data/saxs_computation/sr/1srs/1srs.fit
pddf	/app/data/pr_computation/sr/1srs/1srs.pr.out
profile	/app/data/saxs_computation/sr/1srs/1srs.dat

SERUM RESPONSE FACTOR (SRF) CORE COMPLEXED WITH SPECIFIC SRE DNA

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

PROTEIN (SERUM RESPONSE FACTOR (SRF))

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

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)