SAXSdb — 6ghb

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

Regulatory protein Spx

Bacillus subtilis (strain 168)

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–131	Not recorded	UPF0413 protein GK0824 × 1 （Q5L1S1） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na-HEPES pH 7.5, MgCl2 and PEG400	Resolution 3.10 Å R-free 0.266
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–131	Not recorded	UPF0413 protein GK0824 × 1 （Q5L1S1） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na-HEPES pH 7.5, MgCl2 and PEG400	Resolution 3.10 Å R-free 0.266

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 6GHB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z3E Crystal Structure of Spx in Complex with the C-terminal Domain of the RNA Polymerase Alpha Subunit Deposited 2005-03-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa） Fragment：transcription regulator	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；273 K；lithium sulfate, ammonium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 273K	Resolution 1.50 Å R-free 0.220
3GFK Crystal structure of Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex Deposited 2009-02-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；295 K；vapor diffusion against 6% (w/v) PEG 6000, 100 mM sodium acetate, pH 5.0, 10 micromolar CuCl2, protein concentration 11.5 mg/mL, temperature 295K	Resolution 2.30 Å R-free 0.282
3IHQ Crystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras Deposited 2009-07-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa）	Mutation：C10S	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；273 K；25-30% PEG 4000, 0.1 M sodium citrate, 0.1 M magnesium chloride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.90 Å R-free 0.278
6GHO Crystal structure of Spx in complex with YjbH Deposited 2018-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 3350, MgCl2 and Bis-Tris pH 6.0	Resolution 1.79 Å R-free 0.221

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

View Construct and Data Evidence

UniProt name	SPX_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–132； UniProt 1–131 Author chain C； PDBConstruct 2–132； UniProt 1–131

UPF0413 protein GK0824

Geobacillus kaustophilus (strain HTA426)

UniProt Q5L1S1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–297	Not recorded	Regulatory protein Spx × 1 （O31602） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na-HEPES pH 7.5, MgCl2 and PEG400	Resolution 3.10 Å R-free 0.266
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–297	Not recorded	Regulatory protein Spx × 1 （O31602） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na-HEPES pH 7.5, MgCl2 and PEG400	Resolution 3.10 Å R-free 0.266

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 6GHB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GHO Crystal structure of Spx in complex with YjbH Deposited 2018-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–297（297 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 3350, MgCl2 and Bis-Tris pH 6.0	Resolution 1.79 Å R-free 0.221

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

View Construct and Data Evidence

UniProt name	Y824_GEOKA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–298； UniProt 1–297 Author chain D； PDBConstruct 2–298； UniProt 1–297

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	6ghb
Deposition date deposition_date	2018-05-06
Structure title title	Crystal structure of Spx in complex with YjbH (oxidized)
Keywords keywords	Regulatory protein spx Adaptor protein YjbH, PROTEIN BINDING; PROTEIN BINDING
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	39.79 Å
Radius of gyration Rg (electron density) rg_electron	39.94 Å
Forward intensity I(0) i0	109351000.00
Molecular weight molecular_weight	87255.0 kDa
Excluded volume excluded_volume	110190 Å³
Envelope volume envelope_volume	150460 Å³
Hydration-shell volume shell_volume	32787 Å³
Envelope diameter envelope_diameter	134.4 Å
Shell Rg shell_rg	43.31 Å
Envelope Rg envelope_rg	38.66 Å
Shape Rg shape_rg	39.94 Å
Total Rg total_rg	40.13 Å
Total atoms total_atoms	6142
Residues n_residues	769
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	127.9 Å
Rg (real space) rg_real	40.23 Å
Rg uncertainty (real space) rg_real_error	1.32 Å
I(0) (real space) i0_real	1.0940e+08
I(0) uncertainty (real space) i0_real_error	2.0630e+06
Rg (reciprocal space) rg_reciprocal	39.97 Å
I(0) (reciprocal space) i0_reciprocal	109300000.0000
Solution quality estimate total_estimate	0.7455
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.358
Kurtosis Kurtosis kurtosis	-0.850
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13750000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.621; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.562; Smooth: 0.263

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Regulatory protein Spx
Molecular weight formula_weight	15639.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6155

SMVTLYTSPSCTSCRKARAWLEEHEIPFVERNIFSEPLSIDEIKQILRMTEDGTDEIISTRSKVFQKLNVNVESMPLQDLYRLINEHPGLLRRPIIIDEKRLQVGYNEDEIRRFLPRKVRSFQLREAQRLAN

来源 Source

来源生物 organism	Bacillus subtilis (strain 168)
NCBI Class编号 ncbi_taxonomy_id	224308
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	UPF0413 protein GK0824
Molecular weight formula_weight	33716.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SMSEKFAGKTTSTCYPSQPLGNTNKPLELYLFIDPLCPECWGLEPVIKKLTIEYGRFFTLRHILSGTWATWSARKGTKPEAMAKAWEWAANRTGMSCDGSVWLENPISSPFAPSLAIKAAEMQGKRAGLRFLRKLQEQLFLEKQNVADLSVLAECAVKAGLDVDEFLRDMHSPGAAKAFQCDLKITSEMDVDEIPTLVLFNENIEDEGIKISGCYPYDIYVELIAEMLGFHPEPSSPPPLESFLSHFKFVATKEVAVVYNWTIQEAETEMKKLQLKQKVERVPVKHGTFWRYIDDSRP

来源 Source

来源生物 organism	Geobacillus kaustophilus (strain HTA426)
NCBI Class编号 ncbi_taxonomy_id	235909
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ghba1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.12 — ArsC-like

Domain ID domain_id	d6ghba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ghbc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.12 — ArsC-like

Domain ID domain_id	d6ghbc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	6ghbA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6ghbC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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8. Citations (1)

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Unit-cell length a length_a	85.596 Å
Unit-cell length b length_b	88.704 Å
Unit-cell length c length_c	117.467 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.104 Å
Low-resolution limit resolution_low	48.429 Å
R factor r_factor	0.2260
R_work r_work	0.2216
R_free r_free	0.2659

fit	/app/data/saxs_computation/gh/6ghb/6ghb.fit
pddf	/app/data/pr_computation/gh/6ghb/6ghb.pr.out
profile	/app/data/saxs_computation/gh/6ghb/6ghb.dat

Crystal structure of Spx in complex with YjbH (oxidized)

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

Regulatory protein Spx

State in the Current Structure

Other States of the Same Protein in the Database

UPF0413 protein GK0824

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)