SAXSdb — 1ljm

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

RUNX1 transcription 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 A； UniProt 51–181	Fragment：Runt domain	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；Ethanol, Sodium Chloride, Tris-HCl, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.50 Å R-free 0.249
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 51–181	Fragment：Runt domain	CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；Ethanol, Sodium Chloride, Tris-HCl, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.50 Å R-free 0.249
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 51–181 Chain B； UniProt 51–181	Fragment：Runt domain	CL CHLORIDE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；Ethanol, Sodium Chloride, Tris-HCl, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.50 Å R-free 0.249
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 51–181	Fragment：Runt domain	CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；Ethanol, Sodium Chloride, Tris-HCl, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.50 Å R-free 0.249

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 1LJM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMO IMMUNOGLOBULIN MOTIF DNA-RECOGNITION AND HETERODIMERIZATION FOR THE PEBP2/CBF RUNT-DOMAIN Deposited 1999-05-11	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 52–178（127 aa） Fragment：CORE-BINDING FACTOR ALPHA B SUBUNIT, RUNT DOMAIN	Mutation：C81S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；310 K；Ionic strength (raw mmCIF value) 10mM；Pressure 1 NMR sample composition 96% H2O/4% D2O	Resolution not provided
1CO1 FOLD OF THE CBFA Deposited 1999-05-31	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–175（115 aa） Fragment：RUNT DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K	Resolution not provided
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain Q 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1H9D Aml1/cbf-beta/dna complex Deposited 2001-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.271
1H9D Aml1/cbf-beta/dna complex Deposited 2001-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 50–183（134 aa） Fragment：RUNT DOMAIN RESIDUES 50-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.271

4 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RUNX1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 51–181 Author chain B； PDBConstruct 1–131； UniProt 51–181

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	1ljm
Deposition date deposition_date	2002-04-22
Structure title title	DNA recognition is mediated by conformational transition and by DNA bending
Keywords keywords	immunoglobulin fold, beta-sandwich, TRANSCRIPTION; TRANSCRIPTION
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	19.24 Å
Radius of gyration Rg (electron density) rg_electron	18.02 Å
Forward intensity I(0) i0	11738400.00
Molecular weight molecular_weight	25152.0 kDa
Excluded volume excluded_volume	31396 Å³
Envelope volume envelope_volume	37163 Å³
Hydration-shell volume shell_volume	17458 Å³
Envelope diameter envelope_diameter	61.3 Å
Shell Rg shell_rg	23.91 Å
Envelope Rg envelope_rg	18.24 Å
Shape Rg shape_rg	17.99 Å
Total Rg total_rg	19.02 Å
Total atoms total_atoms	1762
Residues n_residues	228
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	61.1 Å
Rg (real space) rg_real	19.14 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.1740e+07
I(0) uncertainty (real space) i0_real_error	1.5760e+05
Rg (reciprocal space) rg_reciprocal	19.15 Å
I(0) (reciprocal space) i0_reciprocal	11740000.0000
Solution quality estimate total_estimate	0.9011
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.161
Kurtosis Kurtosis kurtosis	-0.455
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2037000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.984

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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	RUNX1 transcription factor
Molecular weight formula_weight	14579.7 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	1963

MVEVLADHPGELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRHRQ

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

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	201

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ljma_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.6 — RUNT domain

Domain ID domain_id	d1ljmb_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.6 — RUNT domain

CATH v4.4 (2 domains)

Domain ID domain_id	1ljmA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

Domain ID domain_id	1ljmB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

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8. Citations (1)

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Unit-cell length a length_a	121.230 Å
Unit-cell length b length_b	121.230 Å
Unit-cell length c length_c	186.330 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	43.000 Å
R factor r_factor	0.1947
R_work r_work	0.1930
R_free r_free	0.2490

fit	/app/data/saxs_computation/lj/1ljm/1ljm.fit
pddf	/app/data/pr_computation/lj/1ljm/1ljm.pr.out
profile	/app/data/saxs_computation/lj/1ljm/1ljm.dat

DNA recognition is mediated by conformational transition and by DNA bending

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

RUNX1 transcription 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