SAXSdb — 9x8z

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

PqqD family protein

Paenibacillus alginolyticus

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 1–89	Not recorded	LppA-leader × 1 （A0ABT4G8U6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% (w/v) PEG 1000, 100mM Potassium phosphate monobasic/Sodium phosphate dibasic, pH 6.2, 200mM Sodium chloride	Resolution 2.10 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–89	Not recorded	LppA-leader × 1 （A0ABT4G8U6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% (w/v) PEG 1000, 100mM Potassium phosphate monobasic/Sodium phosphate dibasic, pH 6.2, 200mM Sodium chloride	Resolution 2.10 Å R-free 0.249

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0ABT4G916_9BACL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 19–107； UniProt 1–89 Author chain D； PDBConstruct 19–107； UniProt 1–89

LppA-leader

Paenibacillus alginolyticus

UniProt A0ABT4G8U6

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 1–27	Not recorded	PqqD family protein × 1 （A0ABT4G916）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% (w/v) PEG 1000, 100mM Potassium phosphate monobasic/Sodium phosphate dibasic, pH 6.2, 200mM Sodium chloride	Resolution 2.10 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–27	Not recorded	PqqD family protein × 1 （A0ABT4G916）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；20% (w/v) PEG 1000, 100mM Potassium phosphate monobasic/Sodium phosphate dibasic, pH 6.2, 200mM Sodium chloride	Resolution 2.10 Å R-free 0.249

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0ABT4G8U6_9BACL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–27； UniProt 1–27 Author chain C； PDBConstruct 1–27； UniProt 1–27

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	9x8z
Deposition date deposition_date	2025-10-20
Structure title title	LppB in Complex with LppA leader peptide
Keywords keywords	RRE, Complex, Leader peptide, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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	21.35 Å
Radius of gyration Rg (electron density) rg_electron	20.56 Å
Forward intensity I(0) i0	10795300.00
Molecular weight molecular_weight	24416.0 kDa
Excluded volume excluded_volume	30553 Å³
Envelope volume envelope_volume	37459 Å³
Hydration-shell volume shell_volume	16284 Å³
Envelope diameter envelope_diameter	75.2 Å
Shell Rg shell_rg	25.75 Å
Envelope Rg envelope_rg	21.10 Å
Shape Rg shape_rg	20.57 Å
Total Rg total_rg	21.33 Å
Total atoms total_atoms	1715
Residues n_residues	212
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	71.9 Å
Rg (real space) rg_real	21.49 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.0800e+07
I(0) uncertainty (real space) i0_real_error	1.4830e+05
Rg (reciprocal space) rg_reciprocal	21.47 Å
I(0) (reciprocal space) i0_reciprocal	10800000.0000
Solution quality estimate total_estimate	0.7731
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.480
Kurtosis Kurtosis kurtosis	-0.351
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4215000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.000

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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	PqqD family protein
Molecular weight formula_weight	12151.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D
Atom count atom_count	1814

MADLTGSSHHHHHHSQDPMTQYLRMNDYESIQLDMEWIILNTDEYTLTKLNGVGGFCWSLLGAAQTVGSISEAIRKEYEFVNETVEEDIEAFLNDMIGRGLVQHAVS

来源 Source

来源生物 organism	Paenibacillus alginolyticus
NCBI Class编号 ncbi_taxonomy_id	59839
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	LppA-leader
Molecular weight formula_weight	3314.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C

MEENTKREQKLYARPMVLSQQPVRFET

来源 Source

来源生物 organism	Paenibacillus alginolyticus
NCBI Class编号 ncbi_taxonomy_id	59839
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

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8. Citations (1)

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Unit-cell length a length_a	52.858 Å
Unit-cell length b length_b	55.595 Å
Unit-cell length c length_c	83.866 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	orthorhombic

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	32.850 Å
R factor r_factor	0.2057
R_work r_work	0.2009
R_free r_free	0.2494

fit	/app/data/saxs_computation/x8/9x8z/9x8z.fit
pddf	/app/data/pr_computation/x8/9x8z/9x8z.pr.out
profile	/app/data/saxs_computation/x8/9x8z/9x8z.dat

LppB in Complex with LppA leader peptide

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

PqqD family protein

State in the Current Structure

Other States of the Same Protein in the Database

LppA-leader

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)