SAXSdb — 1cmo

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

POLYOMAVIRUS ENHANCER BINDING PROTEIN 2

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 52–178	Fragment：CORE-BINDING FACTOR ALPHA B SUBUNIT, RUNT DOMAIN Mutation：C81S	No other associated polymer	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

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 1CMO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CO1 FOLD OF THE CBFA Deposited 1999-05-31	Different construct Different mutation/modification Different experimental conditions	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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different experimental method 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 mutation/modification Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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
1LJM DNA recognition is mediated by conformational transition and by DNA bending Deposited 2002-04-22	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 51–181（131 aa） Fragment：Runt domain	Not recorded	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
1LJM DNA recognition is mediated by conformational transition and by DNA bending Deposited 2002-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 51–181（131 aa） Fragment：Runt domain	Not recorded	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
1LJM DNA recognition is mediated by conformational transition and by DNA bending Deposited 2002-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 51–181（131 aa） Fragment：Runt domain Chain B 51–181（131 aa） Fragment：Runt domain	Not recorded	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
1LJM DNA recognition is mediated by conformational transition and by DNA bending Deposited 2002-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 51–181（131 aa） Fragment：Runt domain	Not recorded	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

4 other PDB entries and 13 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 1–127； UniProt 52–178

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	1cmo
Deposition date deposition_date	1999-05-11
Structure title title	IMMUNOGLOBULIN MOTIF DNA-RECOGNITION AND HETERODIMERIZATION FOR THE PEBP2/CBF RUNT-DOMAIN
Keywords keywords	TRANSCRIPTION FACTOR, HEMATOPOIESIS, OSTEOGENESIS, IG-FOLD, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.52 Å
Radius of gyration Rg (electron density) rg_electron	16.14 Å
Forward intensity I(0) i0	5049600000.00
Molecular weight molecular_weight	601010.0 kDa
Excluded volume excluded_volume	751240 Å³
Envelope volume envelope_volume	51573 Å³
Hydration-shell volume shell_volume	20887 Å³
Envelope diameter envelope_diameter	70.8 Å
Shell Rg shell_rg	27.55 Å
Envelope Rg envelope_rg	21.73 Å
Shape Rg shape_rg	16.12 Å
Total Rg total_rg	16.32 Å
Total atoms total_atoms	85011
Residues n_residues	5461
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	43.8 Å
Rg (real space) rg_real	15.69 Å
Rg uncertainty (real space) rg_real_error	0.06 Å
I(0) (real space) i0_real	4.8230e+09
I(0) uncertainty (real space) i0_real_error	4.0420e+07
Rg (reciprocal space) rg_reciprocal	16.57 Å
I(0) (reciprocal space) i0_reciprocal	5050000000.0000
Solution quality estimate total_estimate	0.6864
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-0.433
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	3.8160
Highest regularization parameter α highest_alpha	258400.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.997; Stabil: 0.978; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cmoa_
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 (1 domains)

Domain ID domain_id	1cmoA00
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	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	POLYOMAVIRUS ENHANCER BINDING PROTEIN 2
Molecular weight formula_weight	14008.9 kDa
Mutation mutation	C81S
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	85011

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)

IMMUNOGLOBULIN MOTIF DNA-RECOGNITION AND HETERODIMERIZATION FOR THE PEBP2/CBF RUNT-DOMAIN

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

POLYOMAVIRUS ENHANCER BINDING PROTEIN 2

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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)

fit	/app/data/saxs_computation/cm/1cmo/1cmo.fit
pddf	/app/data/pr_computation/cm/1cmo/1cmo.pr.out
profile	/app/data/saxs_computation/cm/1cmo/1cmo.dat