SAXSdb — 1bm8

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

TRANSCRIPTION FACTOR MBP1

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 4–102	Fragment：N-TERMINAL DNA-BINDING DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 1.71 Å R-free 0.261

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 1BM8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L3G NMR Structure of the DNA-binding Domain of Cell Cycle Protein, Mbp1(2-124) from Saccharomyces cerevisiae Deposited 2002-02-27	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–124（123 aa） Fragment：DNA-BINDING DOMAIN (RESIDUES 2-124)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.6；288 K NMR sample composition Mbp1 U-15N,13C 40mM Na-Phosphate, 100mM NaCl \| 90% H2O/10% D2O NMR sample composition Mbp1 U-15N, 40mM Na-Phosphate, 100mM NaCl \| 90% H2O/10% D2O	Resolution not provided
1MB1 MBP1 FROM SACCHAROMYCES CEREVISIAE Deposited 1997-07-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.9；pH 6.9	Resolution 2.10 Å R-free 0.290

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

View Construct and Data Evidence

UniProt name	MBP1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 4–102

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	1bm8
Deposition date deposition_date	1998-07-29
Structure title title	DNA-BINDING DOMAIN OF MBP1
Keywords keywords	;CELL CYCLE, CYCLINS, DNA SYNTHESIS, HELIX-TURN-HELIX DNA-BINDING DOMAIN, MULTIWAVELENGTH ANOMALOUS DIFFRACTION, TRANSCRIPTION FACTOR ;; CELL CYCLE
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	13.82 Å
Radius of gyration Rg (electron density) rg_electron	12.47 Å
Forward intensity I(0) i0	2478690.00
Molecular weight molecular_weight	11456.0 kDa
Excluded volume excluded_volume	14594 Å³
Envelope volume envelope_volume	15623 Å³
Hydration-shell volume shell_volume	10659 Å³
Envelope diameter envelope_diameter	41.9 Å
Shell Rg shell_rg	18.21 Å
Envelope Rg envelope_rg	12.71 Å
Shape Rg shape_rg	12.45 Å
Total Rg total_rg	13.88 Å
Total atoms total_atoms	1007
Residues n_residues	99
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	42.9 Å
Rg (real space) rg_real	13.71 Å
Rg uncertainty (real space) rg_real_error	0.17 Å
I(0) (real space) i0_real	2.4790e+06
I(0) uncertainty (real space) i0_real_error	2.0210e+04
Rg (reciprocal space) rg_reciprocal	13.71 Å
I(0) (reciprocal space) i0_reciprocal	2479000.0000
Solution quality estimate total_estimate	0.8897
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.4 Å
Skewness Skewness skewness	0.087
Kurtosis Kurtosis kurtosis	-0.339
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	766200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.995

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bm8a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.34 — DNA-binding domain of Mlu1-box binding protein MBP1
Superfamily Superfamily superfamily	d.34.1 — DNA-binding domain of Mlu1-box binding protein MBP1
Family Family family	d.34.1.1 — DNA-binding domain of Mlu1-box binding protein MBP1

CATH v4.4 (1 domains)

Domain ID domain_id	1bm8A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	10 — Transcription regulator HTH, APSES-type DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	43.350 Å
Unit-cell length b length_b	43.350 Å
Unit-cell length c length_c	124.220 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.710 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2610

Description description	TRANSCRIPTION FACTOR MBP1
Molecular weight formula_weight	11487.2 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	1256

DNA-BINDING DOMAIN OF MBP1

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

TRANSCRIPTION FACTOR MBP1

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	83

fit	/app/data/saxs_computation/bm/1bm8/1bm8.fit
pddf	/app/data/pr_computation/bm/1bm8/1bm8.pr.out
profile	/app/data/saxs_computation/bm/1bm8/1bm8.dat