SAXSdb — 6bie

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

Periplasmic chaperone Spy

Escherichia coli (strain K12)

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 52–147 Chain B； UniProt 52–147	Fragment：UNP RESIDUES 52-147	ZN ZINC ION × 13 CL CHLORIDE ION × 7 IMD IMIDAZOLE × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；273 K；PEG 3000, IMIDAZOLE, ZINC ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.77 Å R-free 0.248
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 52–147 Chain B； UniProt 52–147	Fragment：UNP RESIDUES 52-147	ZN ZINC ION × 26 CL CHLORIDE ION × 14 IMD IMIDAZOLE × 6 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；273 K；PEG 3000, IMIDAZOLE, ZINC ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.77 Å R-free 0.248

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 6BIE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5WNW Chaperone Spy bound to Im7 6-45 ensemble Deposited 2017-08-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 52–147（96 aa） Fragment：UNP residues 52-147 Chain B 52–147（96 aa） Fragment：UNP residues 52-147	Not recorded	IMD IMIDAZOLE × 3 ZN ZINC ION × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；PEG 3000, imidazole, zinc acetate	Resolution 1.79 Å R-free 0.238
5WO1 Chaperone Spy H96L bound to Im7 L18A L19A L37A (Im7 un-modeled) Deposited 2017-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 52–147（96 aa） Fragment：UNP residues 52-147 Chain B 52–147（96 aa） Fragment：UNP residues 52-147	Not recorded	IMD IMIDAZOLE × 5 ZN ZINC ION × 27 CL CHLORIDE ION × 2 GLU GLUTAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；PEG 3000, imidazole, zinc acetate	Resolution 1.87 Å R-free 0.248
5WO2 Chaperone Spy bound to Casein Fragment (Casein un-modeled) Deposited 2017-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 52–147（96 aa） Fragment：UNP residues 52-147 Chain B 52–147（96 aa） Fragment：UNP residues 52-147	Not recorded	IMD IMIDAZOLE × 6 ZN ZINC ION × 16 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；PEG 3000, imidazole, zinc acetate	Resolution 1.77 Å R-free 0.252
5WO3 Chaperone Spy bound to Im7 (Im7 un-modeled) Deposited 2017-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 52–147（96 aa） Fragment：UNP residues 52-147 Chain B 52–147（96 aa） Fragment：UNP residues 52-147	Not recorded	ZN ZINC ION × 12 CL CHLORIDE ION × 2 IMD IMIDAZOLE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；PEG 3000, imidazole, zinc acetate	Resolution 1.87 Å R-free 0.253
6OWX Spy H96L:Im7 L18pI-Phe complex; multiple anomalous datasets contained herein for element identification Deposited 2019-05-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 52–147（96 aa） Chain B 52–147（96 aa）	Not recorded	ZN ZINC ION × 13 CL CHLORIDE ION × 2 IMD IMIDAZOLE × 5 IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-34% PEG 3000, 70-270 mM zinc acetate, and 0.1 M imidazole, pH 8.0	Resolution 2.06 Å R-free 0.277
6OWY Spy H96L:Im7 K20pI-Phe complex; multiple anomalous datasets contained herein for element identification Deposited 2019-05-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 52–147（96 aa） Chain B 52–147（96 aa）	Not recorded	ZN ZINC ION × 11 CL CHLORIDE ION × 2 IMD IMIDAZOLE × 3 IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-34% PEG 3000, 70-270 mM zinc acetate, and 0.1 M imidazole, pH 8.0	Resolution 2.07 Å R-free 0.273
6OWZ Spy H96L:Im7 L19pI-Phe complex; multiple anomalous datasets contained herein for element identification Deposited 2019-05-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 52–147（96 aa） Chain B 52–147（96 aa）	Not recorded	ZN ZINC ION × 11 CL CHLORIDE ION × 2 IMD IMIDAZOLE × 3 IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-34% PEG 3000, 70-270 mM zinc acetate, and 0.1 M imidazole, pH 8.0	Resolution 2.05 Å R-free 0.255

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–97； UniProt 52–147 Author chain B； PDBConstruct 2–97； UniProt 52–147

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	6bie
Deposition date deposition_date	2017-11-01
Structure title title	MISREADING CHAPERONE-SUBSTRATE COMPLEXES FROM RANDOM NOISE
Keywords keywords	CHAPERONE; CHAPERONE
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	21.19 Å
Radius of gyration Rg (electron density) rg_electron	20.65 Å
Forward intensity I(0) i0	12648300.00
Molecular weight molecular_weight	24342.0 kDa
Excluded volume excluded_volume	29403 Å³
Envelope volume envelope_volume	38926 Å³
Hydration-shell volume shell_volume	16738 Å³
Envelope diameter envelope_diameter	68.7 Å
Shell Rg shell_rg	25.72 Å
Envelope Rg envelope_rg	20.13 Å
Shape Rg shape_rg	20.66 Å
Total Rg total_rg	21.30 Å
Total atoms total_atoms	3300
Residues n_residues	194
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	66.7 Å
Rg (real space) rg_real	21.24 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.2650e+07
I(0) uncertainty (real space) i0_real_error	1.7880e+05
Rg (reciprocal space) rg_reciprocal	21.23 Å
I(0) (reciprocal space) i0_reciprocal	12650000.0000
Solution quality estimate total_estimate	0.9041
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.518
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1776000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Periplasmic chaperone Spy
Molecular weight formula_weight	11540.3 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	3689

SFKDLNLTDAQKQQIREIMKGQRDQMKRPPLEERRAMHDIIASDTFDKVKAEAQIAKMEEQRKANMLAHMETQNKIYNILTPEQKKQFNANFEKRLT

来源 Source

来源生物 organism	Escherichia coli (strain K12)
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6bieA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1490 —

Domain ID domain_id	6bieB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1490 —

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8. Citations (1)

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Unit-cell length a length_a	42.960 Å
Unit-cell length b length_b	42.960 Å
Unit-cell length c length_c	258.169 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	16

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	64.540 Å
R factor r_factor	0.1790
R_work r_work	0.1754
R_free r_free	0.2478

fit	/app/data/saxs_computation/bi/6bie/6bie.fit
pddf	/app/data/pr_computation/bi/6bie/6bie.pr.out
profile	/app/data/saxs_computation/bi/6bie/6bie.dat

MISREADING CHAPERONE-SUBSTRATE COMPLEXES FROM RANDOM NOISE

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

Periplasmic chaperone Spy

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