SAXSdb — 5t5k

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

DNA-binding protein HMf-2

Methanothermus fervidus

UniProt P19267

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 × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts	Chain A； UniProt 1–69 Chain B； UniProt 1–69 Chain C； UniProt 1–69 Chain D； UniProt 1–69 Chain E； UniProt 1–69 Chain F； UniProt 1–69	Not recorded	DNA (90-MER) × 1 DNA (90-MER) × 1 CAC CACODYLATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289.15 K；100 mM MgAc, 50 mM Na Cacodylate pH 6.5, 10% PEG 400 under silicon oil	Resolution 4.00 Å R-free 0.262

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 5T5K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A7W CRYSTAL STRUCTURE OF THE HISTONE HMFB FROM METHANOTHERMUS FERVIDUS Deposited 1998-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–69（69 aa）	Not recorded	ZN ZINC ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å R-free 0.248
1B6W CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS Deposited 1999-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–69（69 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.05 Å R-free 0.260
1BFM HISTONE B FROM METHANOTHERMUS FERVIDUS Deposited 1995-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–69（69 aa） Chain B 1–69（69 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

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

View Construct and Data Evidence

UniProt name	HMFB_METFE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 1–69 Author chain B； PDBConstruct 1–69； UniProt 1–69 Author chain C； PDBConstruct 1–69； UniProt 1–69 Author chain D； PDBConstruct 1–69； UniProt 1–69 Author chain E； PDBConstruct 1–69； UniProt 1–69 Author chain F； PDBConstruct 1–69； UniProt 1–69

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	5t5k
Deposition date deposition_date	2016-08-31
Structure title title	Structure of histone-based chromatin in Archaea
Keywords keywords	Nucleosome, Chromatin, Archaea Histones, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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	38.12 Å
Radius of gyration Rg (electron density) rg_electron	35.57 Å
Forward intensity I(0) i0	291219000.00
Molecular weight molecular_weight	100830.0 kDa
Excluded volume excluded_volume	110420 Å³
Envelope volume envelope_volume	168870 Å³
Hydration-shell volume shell_volume	40107 Å³
Envelope diameter envelope_diameter	107.0 Å
Shell Rg shell_rg	41.68 Å
Envelope Rg envelope_rg	34.53 Å
Shape Rg shape_rg	35.43 Å
Total Rg total_rg	36.17 Å
Total atoms total_atoms	6831
Residues n_residues	584
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	107.6 Å
Rg (real space) rg_real	37.96 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	2.9120e+08
I(0) uncertainty (real space) i0_real_error	4.8570e+06
Rg (reciprocal space) rg_reciprocal	38.06 Å
I(0) (reciprocal space) i0_reciprocal	291200000.0000
Solution quality estimate total_estimate	0.8489
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.046
Kurtosis Kurtosis kurtosis	-0.829
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8293000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 1.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.049

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA-binding protein HMf-2
Molecular weight formula_weight	7683.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6831

MELPIAPIGRIIKDAGAERVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDIELAVRRFKK

来源 Source

来源生物 organism	Methanothermus fervidus
NCBI Class编号 ncbi_taxonomy_id	2180
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA (90-MER)
Molecular weight formula_weight	27688.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TATGAACCGTACTGTCGTCTGCGGCCTTTGATTATCAATTAAAGCGTTCTACGGCGTTTTTGATCGCTCAACTGTGCGAGCTAGATCTCA

Entity 3 Entity 3 polymer

Description description	DNA (90-MER)
Molecular weight formula_weight	27827.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TATGAGATCTAGCTCGCACAGTTGAGCGATCAAAAACGCCGTAGAACGCTTTAATTGATAATCAAAGGCCGCAGACGACAGTACGGTTCA

Entity 4 Entity 4 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	3

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5t5kA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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8. Citations (1)

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Unit-cell length a length_a	99.454 Å
Unit-cell length b length_b	99.454 Å
Unit-cell length c length_c	171.730 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	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	4.000 Å
Low-resolution limit resolution_low	19.760 Å
R factor r_factor	0.2165
R_work r_work	0.2144
R_free r_free	0.2618

fit	/app/data/saxs_computation/t5/5t5k/5t5k.fit
pddf	/app/data/pr_computation/t5/5t5k/5t5k.pr.out
profile	/app/data/saxs_computation/t5/5t5k/5t5k.dat

Structure of histone-based chromatin in Archaea

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

DNA-binding protein HMf-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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)