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1bfm

HISTONE B FROM METHANOTHERMUS FERVIDUS

Method: SOLUTION NMR Dmax: 57.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HISTONE B

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–69 Chain B； UniProt 1–69 Not recorded No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions 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 1BFM 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 ligand/ion Different experimental method 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 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）
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
5T5K Structure of histone-based chromatin in Archaea Deposited 2016-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octameric
Chain A 1–69（69 aa）
Chain B 1–69（69 aa）
Chain C 1–69（69 aa）
Chain D 1–69（69 aa）
Chain E 1–69（69 aa）
Chain F 1–69（69 aa）
Not recorded 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

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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1bfm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bfm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bfm
Deposition date deposition_date1995-09-28
Structure title titleHISTONE B FROM METHANOTHERMUS FERVIDUS
Keywords keywordsARCHAEAL HISTONE PROTEIN, DNA BINDING PROTEIN HMF-2, HISTONE PROTEIN; HISTONE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.23 Å
Radius of gyration Rg (electron density) rg_electron15.76 Å
Forward intensity I(0) i03453120000.00
Molecular weight molecular_weight506220.0 kDa
Excluded volume excluded_volume639580 ų
Envelope volume envelope_volume39277 ų
Hydration-shell volume shell_volume18320 ų
Envelope diameter envelope_diameter65.2 Å
Shell Rg shell_rg24.40 Å
Envelope Rg envelope_rg18.46 Å
Shape Rg shape_rg15.74 Å
Total Rg total_rg15.91 Å
Total atoms total_atoms73854
Residues n_residues4554
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.7 Å
Rg (real space) rg_real16.31 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real3.4530e+09
I(0) uncertainty (real space) i0_real_error4.7540e+07
Rg (reciprocal space) rg_reciprocal16.31 Å
I(0) (reciprocal space) i0_reciprocal3453000000.0000
Solution quality estimate total_estimate0.5869
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary15.5 Å
Skewness Skewness skewness0.501
Kurtosis Kurtosis kurtosis-0.076
Angular range angular_range— – 0.4900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha985300.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.561; Stabil: 0.997; Sysdev: 0.353; Positv: 1.000; Valcen: 0.893; 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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1bfma_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.2 — Archaeal histone
Domain ID domain_idd1bfmb_
Class classa — All alpha proteins
Fold Fold folda.22 — Histone-fold
Superfamily Superfamily superfamilya.22.1 — Histone-fold
Family Family familya.22.1.2 — Archaeal histone

CATH v4.4 (2 domains)

Domain ID domain_id1bfmA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id1bfmB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
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8. Citations (1)

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9. Files and Curves (10)