SAXSdb — 1b9m

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

PROTEIN (MODE)

Escherichia coli

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 1–262 Chain B； UniProt 1–262	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 1.75 Å R-free 0.279

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 1B9M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B9N REGULATOR FROM ESCHERICHIA COLI Deposited 1999-02-12	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–262（262 aa） Chain B 1–262（262 aa）	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.09 Å R-free 0.286

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MODE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–265； UniProt 1–262 Author chain B； PDBConstruct 4–265； UniProt 1–262

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	1b9m
Deposition date deposition_date	1999-02-12
Structure title title	REGULATOR FROM ESCHERICHIA COLI
Keywords keywords	DNA-BINDING, GENE REGULATION, WINGED HELIX TURN HELIX, MOLYBDATE, OB FOLD, TRANSCRIPTION; TRANSCRIPTION
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	27.98 Å
Radius of gyration Rg (electron density) rg_electron	26.83 Å
Forward intensity I(0) i0	51117100.00
Molecular weight molecular_weight	54949.0 kDa
Excluded volume excluded_volume	68651 Å³
Envelope volume envelope_volume	87087 Å³
Hydration-shell volume shell_volume	27824 Å³
Envelope diameter envelope_diameter	89.5 Å
Shell Rg shell_rg	33.14 Å
Envelope Rg envelope_rg	26.85 Å
Shape Rg shape_rg	26.84 Å
Total Rg total_rg	27.52 Å
Total atoms total_atoms	3841
Residues n_residues	499
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	87.3 Å
Rg (real space) rg_real	27.95 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	5.1120e+07
I(0) uncertainty (real space) i0_real_error	7.3600e+05
Rg (reciprocal space) rg_reciprocal	27.96 Å
I(0) (reciprocal space) i0_reciprocal	51120000.0000
Solution quality estimate total_estimate	0.9057
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.266
Kurtosis Kurtosis kurtosis	-0.503
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9893000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.908

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (MODE)
Molecular weight formula_weight	28731.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4284

GSHMQAEILLTLKLQQKLFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGTITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEAVAQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEATSLQQGQNVTAYFNADSVIIATLC

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	426

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1b9ma1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.8 — N-terminal domain of molybdate-dependent transcriptional regulator ModE

Domain ID domain_id	d1b9ma3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.6 — MOP-like
Family Family family	b.40.6.2 — BiMOP, duplicated molybdate-binding domain

Domain ID domain_id	d1b9ma4
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.6 — MOP-like
Family Family family	b.40.6.2 — BiMOP, duplicated molybdate-binding domain

Domain ID domain_id	d1b9mb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.8 — N-terminal domain of molybdate-dependent transcriptional regulator ModE

Domain ID domain_id	d1b9mb3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.6 — MOP-like
Family Family family	b.40.6.2 — BiMOP, duplicated molybdate-binding domain

Domain ID domain_id	d1b9mb4
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.6 — MOP-like
Family Family family	b.40.6.2 — BiMOP, duplicated molybdate-binding domain

CATH v4.4 (6 domains)

Domain ID domain_id	1b9mA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b9mA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	1b9mA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	1b9mB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b9mB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	1b9mB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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8. Citations (3)

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Unit-cell length a length_a	81.610 Å
Unit-cell length b length_b	127.240 Å
Unit-cell length c length_c	62.990 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	24.150 Å
R factor r_factor	—
R_work r_work	0.2340
R_free r_free	0.2790

fit	/app/data/saxs_computation/b9/1b9m/1b9m.fit
pddf	/app/data/pr_computation/b9/1b9m/1b9m.pr.out
profile	/app/data/saxs_computation/b9/1b9m/1b9m.dat

REGULATOR FROM ESCHERICHIA COLI

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

PROTEIN (MODE)

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