SAXSdb — 4el1

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

Protein disulfide-isomerase

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 18–479	Fragment：oxidized full-length hPDI, UNP residues 18-479	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 9.8；294 K；25% PEG 3350, 0.1M Bis-Tris, 0.2M ammonium acetate, pH 9.8, EVAPORATION, temperature 294K	Resolution 2.88 Å R-free 0.281
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 18–479	Fragment：oxidized full-length hPDI, UNP residues 18-479	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 9.8；294 K；25% PEG 3350, 0.1M Bis-Tris, 0.2M ammonium acetate, pH 9.8, EVAPORATION, temperature 294K	Resolution 2.88 Å R-free 0.281

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 4EL1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BJX HUMAN PROTEIN DISULFIDE ISOMERASE, NMR, 24 STRUCTURES Deposited 1998-06-29	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 136–245（110 aa） Fragment：B DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K	Resolution not provided
1MEK HUMAN PROTEIN DISULFIDE ISOMERASE, NMR, 40 STRUCTURES Deposited 1996-04-16	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–137（120 aa） Fragment：PROLYL 4-HYDROXYLASE BETA SUBUNIT	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1X5C The solution structure of the second thioredoxin-like domain of human Protein disulfide-isomerase Deposited 2005-05-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 368–475（108 aa） Fragment：Thioredoxin like domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.2mM thioredoxin like domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2BJX PROTEIN DISULFIDE ISOMERASE Deposited 1999-01-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 136–245（110 aa） Fragment：B DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Pressure 1	Resolution not provided
2K18 Solution structure of bb' domains of human protein disulfide isomerase Deposited 2008-02-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 135–357（223 aa） Fragment：residues 135-357	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1 NMR sample composition 2 mM [U-99% 13C; U-99% 15N] hPDI-bb, 25 mM sodium phosphate, 70 mM sodium chloride, 0.5 mM EDTA, 5 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM hPDI-bb, 25 mM sodium phosphate, 70 mM sodium chloride, 0.5 mM EDTA, 5 mM DTT, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-99% 15N] hPDI-bb, 25 mM sodium phosphate, 70 mM sodium chloride, 0.5 mM EDTA, 5 mM DTT, 12 mg/mL Pf1 phages, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3BJ5 Alternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain Deposited 2007-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 230–368（139 aa） Fragment：;b'x domain, UNPR residues 230-368 ;	Mutation：I272A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295.15 K；2.95M Ammonium sulfate, 0.2M NaCl, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 2.20 Å R-free 0.255
3UEM Crystal structure of human PDI bb'a' domains Deposited 2011-10-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 137–479（343 aa） Fragment：;bb'a' domains ;	Not recorded	D1D (4S,5S)-1,2-DITHIANE-4,5-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；25%(w/v) PEG3350, 0.1M Tris-HCl, 0.2M ammonium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.29 Å R-free 0.280
4EKZ Crystal structure of reduced hPDI (abb'xa') Deposited 2012-04-10	Different construct Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–479（462 aa） Fragment：reduced full-length hPDI, UNP residues 18-479	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9.8；294 K；25% PEG 3350, 0.1M Bis-Tris, 0.2M ammonium acetate, pH 9.8, EVAPORATION, temperature 294K	Resolution 2.51 Å R-free 0.250
4JU5 Crystal structure of the dimeric form of the bb' domains of human protein disulfide isomerase Deposited 2013-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 135–367（233 aa） Fragment：;bb' domain ; Chain B 135–367（233 aa） Fragment：;bb' domain ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；25% (w/v) polyethylene glycol 1500, 25 mM sodium malonate, 37.5 mM imidazole, 37.5 mM boric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.28 Å R-free 0.290
6I7S Microsomal triglyceride transfer protein Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 18–508（491 aa）	Not recorded	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 11 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 7 PEG DI(HYDROXYETHYL)ETHER × 2 PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M Tris pH 8.25, 0.2 M Li2SO4, 32% v/v PEG 400, 2% Polypropylene glycol P425	Resolution 2.50 Å R-free 0.257
6I7S Microsomal triglyceride transfer protein Deposited 2018-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–508（491 aa）	Not recorded	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 8 PGE TRIETHYLENE GLYCOL × 5 SO4 SULFATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 7 PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 1 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M Tris pH 8.25, 0.2 M Li2SO4, 32% v/v PEG 400, 2% Polypropylene glycol P425	Resolution 2.50 Å R-free 0.257
7ZSC Crystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 18–508（491 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；278 K；20% (w/v) PEG4000, 0.2 M lithium sulfate, 0.1 M MES, 3% methanol	Resolution 3.85 Å R-free 0.278
7ZSC Crystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 18–508（491 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；278 K；20% (w/v) PEG4000, 0.2 M lithium sulfate, 0.1 M MES, 3% methanol	Resolution 3.85 Å R-free 0.278
8EOJ Microsomal triglyceride transfer protein Deposited 2022-10-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–508（508 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
8GDY Crystal structure of the human PDI first domain with 9 mutations Deposited 2023-03-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–137（120 aa）	Mutation：K31R, K42R, K57R, K65R, K69R, K71R, K114R, K130R, K131R	SCN THIOCYANATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6；277 K；0.1 M potassium thiocyanate, 0.1 M MES, and 24% (w/v) PEG 20k	Resolution 2.05 Å R-free 0.239
8GDY Crystal structure of the human PDI first domain with 9 mutations Deposited 2023-03-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–137（120 aa）	Mutation：K31R, K42R, K57R, K65R, K69R, K71R, K114R, K130R, K131R	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6；277 K；0.1 M potassium thiocyanate, 0.1 M MES, and 24% (w/v) PEG 20k	Resolution 2.05 Å R-free 0.239

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDIA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–482； UniProt 18–479 Author chain B； PDBConstruct 21–482； UniProt 18–479

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	4el1
Deposition date deposition_date	2012-04-10
Structure title title	Crystal structure of oxidized hPDI (abb'xa')
Keywords keywords	;abb'a' domains, "CGHC" active sites, Horseshoe shape, enzyme, a redox-regulated chaperone, Endoplasmic reticulum, 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	38.18 Å
Radius of gyration Rg (electron density) rg_electron	37.66 Å
Forward intensity I(0) i0	153154000.00
Molecular weight molecular_weight	101670.0 kDa
Excluded volume excluded_volume	128050 Å³
Envelope volume envelope_volume	185280 Å³
Hydration-shell volume shell_volume	43428 Å³
Envelope diameter envelope_diameter	123.9 Å
Shell Rg shell_rg	41.45 Å
Envelope Rg envelope_rg	36.41 Å
Shape Rg shape_rg	37.65 Å
Total Rg total_rg	37.96 Å
Total atoms total_atoms	7190
Residues n_residues	904
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	120.4 Å
Rg (real space) rg_real	38.11 Å
Rg uncertainty (real space) rg_real_error	1.21 Å
I(0) (real space) i0_real	1.5320e+08
I(0) uncertainty (real space) i0_real_error	2.7090e+06
Rg (reciprocal space) rg_reciprocal	38.16 Å
I(0) (reciprocal space) i0_reciprocal	153200000.0000
Solution quality estimate total_estimate	0.8923
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.0 Å
Skewness Skewness skewness	0.196
Kurtosis Kurtosis kurtosis	-0.597
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7651000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.822

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein disulfide-isomerase
Molecular weight formula_weight	54204.9 kDa
EC 编号 ec_number	5.3.4.1
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	7222

MHHHHHHSSGLEVLFQGPGSDAPEEEDHVLVLRKSNFAEALAAHKYLLVEFYAPWCGHCKALAPEYAKAAGKLKAEGSEIRLAKVDATEESDLAQQYGVRGYPTIKFFRNGDTASPKEYTAGREADDIVNWLKKRTGPAATTLPDGAAAESLVESSEVAVIGFFKDVESDSAKQFLQAAEAIDDIPFGITSNSDVFSKYQLDKDGVVLFKKFDEGRNNFEGEVTKENLLDFIKHNQLPLVIEFTEQTAPKIFGGEIKTHILLFLPKSVSDYDGKLSNFKTAAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAVRLITLEEEMTKYKPESEELTAERITEFCHRFLEGKIKPHLMSQELPEDWDKQPVKVLVGKNFEDVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDHENIVIAKMDSTANEVEAVKVHSFPTLKFFPASADRTVIDYNGERTLDGFKKFLESGGQDGAG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4el1A01
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	4el1A02
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	4el1A03
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	4el1A04
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	4el1B01
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	4el1B02
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	4el1B03
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	4el1B04
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	160.748 Å
Unit-cell length b length_b	34.014 Å
Unit-cell length c length_c	156.959 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.883 Å
Low-resolution limit resolution_low	29.837 Å
R factor r_factor	0.2623
R_work r_work	0.2611
R_free r_free	0.2815

fit	/app/data/saxs_computation/el/4el1/4el1.fit
pddf	/app/data/pr_computation/el/4el1/4el1.pr.out
profile	/app/data/saxs_computation/el/4el1/4el1.dat

Crystal structure of oxidized hPDI (abb'xa')

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

Protein disulfide-isomerase

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