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1hmf

STRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1

Method: SOLUTION NMR Dmax: 56.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HIGH MOBILITY GROUP PROTEIN FRAGMENT-B

Rattus norvegicus

UniProt P63159

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 88–164 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 1HMF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AAB NMR STRUCTURE OF RAT HMG1 HMGA FRAGMENT Deposited 1995-10-28 Different construct Different mutation/modification Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–83（83 aa） Fragment：FRAGMENT A (RESIDUES 1 - 83)
Mutation：C22S No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1CKT CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX Deposited 1999-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 7–77（71 aa） Fragment：RESIDUES 8-78, DOMAIN A
Not recorded CPT Cisplatin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED HEPES, MAGNESIUM ACETATE, PEG 3350, GLYCEROL AND DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.50 Å R-free 0.239
1HME STRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1 Deposited 1994-02-10 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 88–164（77 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
4QR9 Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA Deposited 2014-06-30 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 × 2 PDB declaration: hexameric
Chain A 8–81（74 aa） Fragment：Residues 8-81
Chain B 8–81（74 aa） Fragment：Residues 8-81
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.025M Sodium Cacodylate 0.020M Magnesium Chloride 2.5% MPD (equilibrated against 40% MPD), pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.234

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HMG1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–77； UniProt 88–164

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 1hmf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1hmf
Deposition date deposition_date1994-03-07
Structure title titleSTRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1
Keywords keywordsDNA-BINDING; DNA-BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.22 Å
Radius of gyration Rg (electron density) rg_electron16.06 Å
Forward intensity I(0) i0898906000.00
Molecular weight molecular_weight263370.0 kDa
Excluded volume excluded_volume333430 ų
Envelope volume envelope_volume38633 ų
Hydration-shell volume shell_volume16657 ų
Envelope diameter envelope_diameter62.8 Å
Shell Rg shell_rg25.89 Å
Envelope Rg envelope_rg20.75 Å
Shape Rg shape_rg16.04 Å
Total Rg total_rg16.32 Å
Total atoms total_atoms37410
Residues n_residues2310
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 dmax56.3 Å
Rg (real space) rg_real16.33 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real8.9890e+08
I(0) uncertainty (real space) i0_real_error1.1370e+07
Rg (reciprocal space) rg_reciprocal16.32 Å
I(0) (reciprocal space) i0_reciprocal898900000.0000
Solution quality estimate total_estimate0.7031
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks4
Primary peak position r_peak_primary13.7 Å
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.730
Angular range angular_range— – 0.4900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha138700.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.505; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.625; 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_idd1hmfa_
Class classa — All alpha proteins
Fold Fold folda.21 — HMG-box
Superfamily Superfamily superfamilya.21.1 — HMG-box
Family Family familya.21.1.1 — HMG-box

CATH v4.4 (1 domains)

Domain ID domain_id1hmfA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily10 — High mobility group box domain
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8. Citations (1)

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9. Files and Curves (10)