SAXSdb — 1bw6

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

PROTEIN (CENTROMERE PROTEIN B)

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 1–56	Fragment：DNA-BINDING DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；303 K；Ionic strength (raw mmCIF value) 400 mM NA2SO4	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 1BW6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HLV CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA Deposited 2000-12-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–129（129 aa） Fragment：DNA BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；MPD, potassium cacodylate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.260
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 540–599（60 aa） Fragment：dimerization domain Chain B 540–599（60 aa） Fragment：dimerization domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.309
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 540–599（60 aa） Fragment：dimerization domain Chain D 540–599（60 aa） Fragment：dimerization domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.309
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 540–599（60 aa） Fragment：dimerization domain Chain B 540–599（60 aa） Fragment：dimerization domain Chain C 540–599（60 aa） Fragment：dimerization domain Chain D 540–599（60 aa） Fragment：dimerization domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.309
6KDR Crystal structure of human NRMT2 in complex with human centromere protein B peptide Deposited 2019-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2–10（9 aa） Chain E 2–10（9 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；291 K；0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000	Resolution 2.11 Å R-free 0.205

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CENPB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–56； UniProt 1–56

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	1bw6
Deposition date deposition_date	1998-09-30
Structure title title	HUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1
Keywords keywords	;CENTROMERE PROTEIN, DNA-BINDING, HELIX-TURN-HELIX, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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	12.96 Å
Radius of gyration Rg (electron density) rg_electron	11.19 Å
Forward intensity I(0) i0	1040100.00
Molecular weight molecular_weight	6540.0 kDa
Excluded volume excluded_volume	8219 Å³
Envelope volume envelope_volume	9627 Å³
Hydration-shell volume shell_volume	7698 Å³
Envelope diameter envelope_diameter	38.4 Å
Shell Rg shell_rg	16.29 Å
Envelope Rg envelope_rg	11.76 Å
Shape Rg shape_rg	11.12 Å
Total Rg total_rg	12.81 Å
Total atoms total_atoms	951
Residues n_residues	56
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	41.4 Å
Rg (real space) rg_real	12.90 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.0400e+06
I(0) uncertainty (real space) i0_real_error	1.0970e+04
Rg (reciprocal space) rg_reciprocal	12.91 Å
I(0) (reciprocal space) i0_reciprocal	1040000.0000
Solution quality estimate total_estimate	0.8844
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.2 Å
Skewness Skewness skewness	0.217
Kurtosis Kurtosis kurtosis	-0.261
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	260000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.986

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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	d1bw6a_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.7 — Centromere-binding

CATH v4.4 (1 domains)

Domain ID domain_id	1bw6A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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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	PROTEIN (CENTROMERE PROTEIN B)
Molecular weight formula_weight	6546.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	951

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

HUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1

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

PROTEIN (CENTROMERE PROTEIN B)

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/bw/1bw6/1bw6.fit
pddf	/app/data/pr_computation/bw/1bw6/1bw6.pr.out
profile	/app/data/saxs_computation/bw/1bw6/1bw6.dat