SAXSdb — 5idr

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

DsbA-like protein

Proteus mirabilis ATCC 29906

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 22–243 Chain B； UniProt 22–243 Chain C； UniProt 22–243	Fragment：UNP residues 22-243	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；293.15 K；2.85 M Sodium malonate pH 5.8, 0.1 M Copper(II) chloride	Resolution 2.56 Å R-free 0.222
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 22–243 Chain E； UniProt 22–243 Chain F； UniProt 22–243	Fragment：UNP residues 22-243	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；293.15 K；2.85 M Sodium malonate pH 5.8, 0.1 M Copper(II) chloride	Resolution 2.56 Å R-free 0.222

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 5IDR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–243（222 aa） Fragment：UNP residues 22-243 Chain B 22–243（222 aa） Fragment：UNP residues 22-243 Chain F 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 22–243（222 aa） Fragment：UNP residues 22-243 Chain D 22–243（222 aa） Fragment：UNP residues 22-243 Chain K 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain E 22–243（222 aa） Fragment：UNP residues 22-243 Chain I 22–243（222 aa） Fragment：UNP residues 22-243 Chain J 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 22–243（222 aa） Fragment：UNP residues 22-243 Chain H 22–243（222 aa） Fragment：UNP residues 22-243 Chain L 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain M 22–243（222 aa） Fragment：UNP residues 22-243 Chain N 22–243（222 aa） Fragment：UNP residues 22-243 Chain R 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain O 22–243（222 aa） Fragment：UNP residues 22-243 Chain P 22–243（222 aa） Fragment：UNP residues 22-243 Chain W 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain Q 22–243（222 aa） Fragment：UNP residues 22-243 Chain U 22–243（222 aa） Fragment：UNP residues 22-243 Chain V 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
4XVW Crystal structure of Proteus mirabilis ScsC in a compact conformation Deposited 2015-01-27	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain T 22–243（222 aa） Fragment：UNP residues 22-243 Chain X 22–243（222 aa） Fragment：UNP residues 22-243 Chain Y 22–243（222 aa） Fragment：UNP residues 22-243	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；2.85 M sodium malonate, 0.1 M Cobalt(II)chloride hexahydrate	Resolution 2.60 Å R-free 0.282
5ID4 Crystal structure of Proteus mirabilis ScsC in an extended conformation Deposited 2016-02-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–243（222 aa） Fragment：UNP residues 22-243	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；32% Jeffamine M-600 pH 7, 0.1 M HEPES pH 8, 2.5 mM Copper(II) chloride	Resolution 2.92 Å R-free 0.263

2 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C2LPE2_PROMI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–224； UniProt 22–243 Author chain B； PDBConstruct 3–224； UniProt 22–243 Author chain C； PDBConstruct 3–224； UniProt 22–243 Author chain D； PDBConstruct 3–224； UniProt 22–243 Author chain E； PDBConstruct 3–224； UniProt 22–243 Author chain F； PDBConstruct 3–224； UniProt 22–243

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	5idr
Deposition date deposition_date	2016-02-24
Structure title title	Crystal structure of Proteus Mirabilis ScsC in a transitional conformation
Keywords keywords	thioredoxin fold, disulfide isomerase, trimer, copper resistance, ISOMERASE; ISOMERASE
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	37.26 Å
Radius of gyration Rg (electron density) rg_electron	37.12 Å
Forward intensity I(0) i0	308725000.00
Molecular weight molecular_weight	145110.0 kDa
Excluded volume excluded_volume	183140 Å³
Envelope volume envelope_volume	231390 Å³
Hydration-shell volume shell_volume	53074 Å³
Envelope diameter envelope_diameter	133.6 Å
Shell Rg shell_rg	42.13 Å
Envelope Rg envelope_rg	37.29 Å
Shape Rg shape_rg	37.12 Å
Total Rg total_rg	37.46 Å
Total atoms total_atoms	20642
Residues n_residues	1315
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	130.8 Å
Rg (real space) rg_real	37.46 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	3.0870e+08
I(0) uncertainty (real space) i0_real_error	5.0040e+06
Rg (reciprocal space) rg_reciprocal	37.34 Å
I(0) (reciprocal space) i0_reciprocal	308700000.0000
Solution quality estimate total_estimate	0.7794
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.5 Å
Skewness Skewness skewness	0.534
Kurtosis Kurtosis kurtosis	-0.130
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	52690000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

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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) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5idrA01
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	5idrB01
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	5idrC01
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	5idrD01
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	5idrE01
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	5idrF01
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	193.054 Å
Unit-cell length b length_b	193.054 Å
Unit-cell length c length_c	105.806 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	48

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.562 Å
Low-resolution limit resolution_low	42.817 Å
R factor r_factor	0.1734
R_work r_work	0.1709
R_free r_free	0.2216

Description description	DsbA-like protein
Molecular weight formula_weight	24800.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	20856

Crystal structure of Proteus Mirabilis ScsC in a transitional conformation

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

DsbA-like protein

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) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Proteus mirabilis ATCC 29906
NCBI Class编号 ncbi_taxonomy_id	525369
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	82

fit	/app/data/saxs_computation/id/5idr/5idr.fit
pddf	/app/data/pr_computation/id/5idr/5idr.pr.out
profile	/app/data/saxs_computation/id/5idr/5idr.dat