4xvw

Crystal structure of Proteus mirabilis ScsC in a compact conformation

Method: X-RAY DIFFRACTION D_max: 245.4 Å Quality: GOOD

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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 F； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 22–243 Chain D； UniProt 22–243 Chain K； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
3	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 22–243 Chain I； UniProt 22–243 Chain J； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
4	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 22–243 Chain H； UniProt 22–243 Chain L； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
5	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain M； UniProt 22–243 Chain N； UniProt 22–243 Chain R； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
6	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain O； UniProt 22–243 Chain P； UniProt 22–243 Chain W； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
7	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain Q； UniProt 22–243 Chain U； UniProt 22–243 Chain V； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
8	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain T； UniProt 22–243 Chain X； UniProt 22–243 Chain Y； UniProt 22–243	Fragment：UNP residues 22-243 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 4XVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
5IDR Crystal structure of Proteus Mirabilis ScsC in a transitional conformation Deposited 2016-02-24	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 C 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；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
5IDR Crystal structure of Proteus Mirabilis ScsC in a transitional conformation Deposited 2016-02-24	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 22–243（222 aa） Fragment：UNP residues 22-243 Chain E 22–243（222 aa） Fragment：UNP residues 22-243 Chain F 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；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 other PDB entries and 3 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 Author chain G； PDBConstruct 3–224； UniProt 22–243 Author chain H； PDBConstruct 3–224； UniProt 22–243 Author chain I； PDBConstruct 3–224； UniProt 22–243 Author chain J； PDBConstruct 3–224； UniProt 22–243 Author chain K； PDBConstruct 3–224； UniProt 22–243 Author chain L； PDBConstruct 3–224； UniProt 22–243 Author chain M； PDBConstruct 3–224； UniProt 22–243 Author chain N； PDBConstruct 3–224； UniProt 22–243 Author chain O； PDBConstruct 3–224； UniProt 22–243 Author chain P； PDBConstruct 3–224； UniProt 22–243 Author chain Q； PDBConstruct 3–224； UniProt 22–243 Author chain R； PDBConstruct 3–224； UniProt 22–243 Author chain T； PDBConstruct 3–224； UniProt 22–243 Author chain U； PDBConstruct 3–224； UniProt 22–243 Author chain V； PDBConstruct 3–224； UniProt 22–243 Author chain W； PDBConstruct 3–224； UniProt 22–243 Author chain X； PDBConstruct 3–224； UniProt 22–243 Author chain Y； 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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4xvw
Deposition date deposition_date	2015-01-27
Structure title title	Crystal structure of Proteus mirabilis ScsC in a compact conformation
Keywords keywords	Thioredoxin fold, disulfide isomerase, trimeric, antimicrobial resistance, swarming motility, 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	72.11 Å
Radius of gyration Rg (electron density) rg_electron	72.12 Å
Forward intensity I(0) i0	4628480000.00
Molecular weight molecular_weight	583020.0 kDa
Excluded volume excluded_volume	732010 Å³
Envelope volume envelope_volume	1198200 Å³
Hydration-shell volume shell_volume	135860 Å³
Envelope diameter envelope_diameter	250.8 Å
Shell Rg shell_rg	77.06 Å
Envelope Rg envelope_rg	69.00 Å
Shape Rg shape_rg	72.14 Å
Total Rg total_rg	72.12 Å
Total atoms total_atoms	82507
Residues n_residues	5131
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	245.4 Å
Rg (real space) rg_real	72.03 Å
Rg uncertainty (real space) rg_real_error	2.13 Å
I(0) (real space) i0_real	4.6280e+09
I(0) uncertainty (real space) i0_real_error	9.9030e+07
Rg (reciprocal space) rg_reciprocal	72.17 Å
I(0) (reciprocal space) i0_reciprocal	4629000000.0000
Solution quality estimate total_estimate	0.8440
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	111.5 Å
Skewness Skewness skewness	0.157
Kurtosis Kurtosis kurtosis	-0.586
Angular range angular_range	— – 0.1100 Å⁻¹
Current regularization parameter α current_alpha	0.0013
Highest regularization parameter α highest_alpha	1018000000.0000
Real-space data points n_real_points	23
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.648

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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) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	4xvwA01
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	4xvwB01
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	4xvwC01
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	4xvwD01
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	4xvwE01
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	4xvwF01
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	4xvwG01
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	4xvwH01
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	4xvwI01
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	4xvwJ01
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	4xvwK01
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	4xvwL00
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	4xvwM01
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	4xvwN01
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	4xvwO01
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	4xvwP01
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	4xvwQ01
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	4xvwR01
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	4xvwT01
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	4xvwU01
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	4xvwV01
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	4xvwW01
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	4xvwX01
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	4xvwY01
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	137.475 Å
Unit-cell length b length_b	163.885 Å
Unit-cell length c length_c	181.936 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	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	91.152 Å
R factor r_factor	0.2540
R_work r_work	0.2484
R_free r_free	0.2818

Description description	DsbA-like protein
Molecular weight formula_weight	24988.0 kDa
Source method src_method	man
Copy count entity_count	24

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,T,U,V,W,X,Y
Atom count atom_count	83204

Crystal structure of Proteus mirabilis ScsC in a compact 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) 24 domains

CATH v4.4 (24 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	281

fit	/app/data/saxs_computation/xv/4xvw/4xvw.fit
pddf	/app/data/pr_computation/xv/4xvw/4xvw.pr.out
profile	/app/data/saxs_computation/xv/4xvw/4xvw.dat