SAXSdb — 1ufi

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

Major centromere autoantigen 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 540–599 Chain B； UniProt 540–599	Fragment：dimerization domain	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 540–599 Chain D； UniProt 540–599	Fragment：dimerization domain	No other associated polymer	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
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 540–599 Chain B； UniProt 540–599 Chain C； UniProt 540–599 Chain D； UniProt 540–599	Fragment：dimerization domain	No other associated polymer	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

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 1UFI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BW6 HUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1 Deposited 1998-09-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–56（56 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 400 mM NA2SO4	Resolution not provided
1HLV CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA Deposited 2000-12-04	Different construct Different mutation/modification Different oligomeric state 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
6KDR Crystal structure of human NRMT2 in complex with human centromere protein B peptide Deposited 2019-07-02	Different construct Different oligomeric state Different ligand/ion 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 3 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 5–64； UniProt 540–599 Author chain B； PDBConstruct 5–64； UniProt 540–599 Author chain C； PDBConstruct 5–64； UniProt 540–599 Author chain D； PDBConstruct 5–64； UniProt 540–599

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	1ufi
Deposition date deposition_date	2003-05-30
Structure title title	Crystal structure of the dimerization domain of human CENP-B
Keywords keywords	dimerization domain, salt bridge, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, DNA BINDING PROTEIN; DNA BINDING 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	18.68 Å
Radius of gyration Rg (electron density) rg_electron	17.44 Å
Forward intensity I(0) i0	8577690.00
Molecular weight molecular_weight	21935.0 kDa
Excluded volume excluded_volume	27586 Å³
Envelope volume envelope_volume	31735 Å³
Hydration-shell volume shell_volume	15621 Å³
Envelope diameter envelope_diameter	60.4 Å
Shell Rg shell_rg	23.00 Å
Envelope Rg envelope_rg	17.76 Å
Shape Rg shape_rg	17.46 Å
Total Rg total_rg	18.29 Å
Total atoms total_atoms	1547
Residues n_residues	188
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	61.2 Å
Rg (real space) rg_real	18.64 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	8.5780e+06
I(0) uncertainty (real space) i0_real_error	9.8380e+04
Rg (reciprocal space) rg_reciprocal	18.65 Å
I(0) (reciprocal space) i0_reciprocal	8578000.0000
Solution quality estimate total_estimate	0.8862
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.9 Å
Skewness Skewness skewness	0.299
Kurtosis Kurtosis kurtosis	-0.344
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2127000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.970

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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) 11 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1ufia1
Class class	a — All alpha proteins
Fold Fold fold	a.30 — ROP-like
Superfamily Superfamily superfamily	a.30.4 — Dimerisation domain of CENP-B
Family Family family	a.30.4.1 — Dimerisation domain of CENP-B

Domain ID domain_id	d1ufia2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ufib_
Class class	a — All alpha proteins
Fold Fold fold	a.30 — ROP-like
Superfamily Superfamily superfamily	a.30.4 — Dimerisation domain of CENP-B
Family Family family	a.30.4.1 — Dimerisation domain of CENP-B

Domain ID domain_id	d1ufic1
Class class	a — All alpha proteins
Fold Fold fold	a.30 — ROP-like
Superfamily Superfamily superfamily	a.30.4 — Dimerisation domain of CENP-B
Family Family family	a.30.4.1 — Dimerisation domain of CENP-B

Domain ID domain_id	d1ufic2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ufid1
Class class	a — All alpha proteins
Fold Fold fold	a.30 — ROP-like
Superfamily Superfamily superfamily	a.30.4 — Dimerisation domain of CENP-B
Family Family family	a.30.4.1 — Dimerisation domain of CENP-B

Domain ID domain_id	d1ufid2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1ufiA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1090 — Dimerisation domain of CENP-B

Domain ID domain_id	1ufiB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1090 — Dimerisation domain of CENP-B

Domain ID domain_id	1ufiC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1090 — Dimerisation domain of CENP-B

Domain ID domain_id	1ufiD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1090 — Dimerisation domain of CENP-B

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8. Citations (1)

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Unit-cell length a length_a	43.707 Å
Unit-cell length b length_b	48.955 Å
Unit-cell length c length_c	100.700 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	19.760 Å
R factor r_factor	0.2360
R_work r_work	0.2322
R_free r_free	0.3085

Description description	Major centromere autoantigen B
Molecular weight formula_weight	7249.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1694

Crystal structure of the dimerization domain of human CENP-B

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

Major centromere autoantigen 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

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) 11 domains

SCOP 2.08 (7 domains)

CATH v4.4 (4 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	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

fit	/app/data/saxs_computation/uf/1ufi/1ufi.fit
pddf	/app/data/pr_computation/uf/1ufi/1ufi.pr.out
profile	/app/data/saxs_computation/uf/1ufi/1ufi.dat