SAXSdb — 1lwm

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

NONHISTONE CHROMOSOMAL PROTEIN 6A

Saccharomyces cerevisiae

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 1–93	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.5；293 K；Ionic strength (raw mmCIF value) 10 mM NaPO4, 100 mM NaCl；Pressure ambient NMR sample composition：1 2mM 15N-labeled NHP6A \| 90% H2O, 10% D2O or 100% D2O NMR sample composition：2mM 13C/15N-labeled NHP6A \| 90% H2O, 10% D2O or 100% D2O	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 1LWM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CG7 HMG PROTEIN NHP6A FROM SACCHAROMYCES CEREVISIAE Deposited 1999-03-27	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–93（93 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；293 K；Ionic strength (raw mmCIF value) 100 mM NACL	Resolution not provided
1J5N Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA Deposited 2002-05-15	Different oligomeric state Different experimental conditions	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–93（93 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；310 K；Ionic strength (raw mmCIF value) 2 mM NaPO4, 10 mM NaCl；Pressure ambient NMR measurement conditions pH 5.8；283 K；Ionic strength (raw mmCIF value) 2 mM NaPO4, 10 mM NaCl；Pressure ambient NMR sample composition protein and DNA unlabeled, 2mM sample 90% H2O, 10% D2O or 100% D2O NMR sample composition Uniform labeling with 15N of protein, DNA unlabeled, 2mM 90% H2O, 10% D2O NMR sample composition Uniform labeling with 15N,13C of protein, DNA unlabeled, 2mM 100% D2O NMR sample composition Uniform labeling with 15N,13C of DNA (both strands), protein unlabeled, 2mM 100% D2O NMR sample composition Uniform labeling with 15N,13C of G-rich DNA strand and protein, C-rich DNA strand unlabeled, 2mM 100% D2O NMR sample composition Uniform labeling with 15N,13C of C-rich DNA strand and protein, G-rich DNA strand unlabeled, 2mM 100% D2O	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NHP6A_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–93； UniProt 1–93

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	1lwm
Deposition date deposition_date	2002-05-31
Structure title title	Solution Structure of the Sequence-Non-Specific HMGB protein NHP6A
Keywords keywords	HMG-BOX, HMGB, ALPHA HELIX, 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	19.66 Å
Radius of gyration Rg (electron density) rg_electron	19.55 Å
Forward intensity I(0) i0	670310000.00
Molecular weight molecular_weight	216210.0 kDa
Excluded volume excluded_volume	271010 Å³
Envelope volume envelope_volume	84491 Å³
Hydration-shell volume shell_volume	26875 Å³
Envelope diameter envelope_diameter	83.7 Å
Shell Rg shell_rg	33.22 Å
Envelope Rg envelope_rg	27.71 Å
Shape Rg shape_rg	19.45 Å
Total Rg total_rg	20.36 Å
Total atoms total_atoms	30780
Residues n_residues	1860
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	75.1 Å
Rg (real space) rg_real	19.88 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	6.7030e+08
I(0) uncertainty (real space) i0_real_error	1.0040e+07
Rg (reciprocal space) rg_reciprocal	19.85 Å
I(0) (reciprocal space) i0_reciprocal	670300000.0000
Solution quality estimate total_estimate	0.7812
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	14.8 Å
Skewness Skewness skewness	0.426
Kurtosis Kurtosis kurtosis	-0.255
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	160500.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.632; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.302; Smooth: 0.954

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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	d1lwma_
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

CATH v4.4 (1 domains)

Domain ID domain_id	1lwmA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

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8. Citations (1)

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Description description	NONHISTONE CHROMOSOMAL PROTEIN 6A
Molecular weight formula_weight	10824.4 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	30780

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/lw/1lwm/1lwm.fit
pddf	/app/data/pr_computation/lw/1lwm/1lwm.pr.out
profile	/app/data/saxs_computation/lw/1lwm/1lwm.dat

Solution Structure of the Sequence-Non-Specific HMGB protein NHP6A

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

NONHISTONE CHROMOSOMAL PROTEIN 6A

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

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)