7zsc

Crystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281)

Method: X-RAY DIFFRACTION Dmax: 130.3 Å Quality: GOOD

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

Prolyl 4-hydroxylase subunit alpha-2

Homo sapiens

UniProt O15460

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 282–535 Not recorded Protein disulfide-isomerase × 1 (P07237) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 282–535 Not recorded Protein disulfide-isomerase × 1 (P07237) 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

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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name P4HA2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 9–262; UniProt 282–535 Author chain B; PDBConstruct 9–262; UniProt 282–535

Protein disulfide-isomerase

Homo sapiens

UniProt P07237

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 C; UniProt 18–508 Not recorded Prolyl 4-hydroxylase subunit alpha-2 × 1 (O15460) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 18–508 Not recorded Prolyl 4-hydroxylase subunit alpha-2 × 1 (O15460) 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

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.

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 2
Chains and sequence ranges Author chain C; PDBConstruct 2–492; UniProt 18–508 Author chain D; PDBConstruct 2–492; UniProt 18–508

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

SAXS profile for 7zsc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7zsc
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7zsc
Deposition date deposition_date2022-05-06
Structure title titleCrystal structure of the heterodimeric human C-P4H-II with truncated alpha subunit (C-P4H-II delta281)
Keywords keywordsCollagen synthesis, PDI, DSBH fold, thioredoxin, dioxygenase, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.44
Radius of gyration Rg (electron density) rg_electron39.07
Forward intensity I(0) i0369939000.00
Molecular weight molecular_weight156980.0 kDa
Excluded volume excluded_volume196650 ų
Envelope volume envelope_volume270220 ų
Hydration-shell volume shell_volume58666 ų
Envelope diameter envelope_diameter136.9
Shell Rg shell_rg43.88
Envelope Rg envelope_rg38.62
Shape Rg shape_rg39.08
Total Rg total_rg39.32
Total atoms total_atoms11091
Residues n_residues1384
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.3
Rg (real space) rg_real39.50
Rg uncertainty (real space) rg_real_error1.18
I(0) (real space) i0_real3.6990e+08
I(0) uncertainty (real space) i0_real_error6.0690e+06
Rg (reciprocal space) rg_reciprocal39.47
I(0) (reciprocal space) i0_reciprocal369900000.0000
Solution quality estimate total_estimate0.8564
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.6
Skewness Skewness skewness0.443
Kurtosis Kurtosis kurtosis-0.035
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33700000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.618

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id7zscA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily620 — q2cbj1_9rhob like domain
Domain ID domain_id7zscB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily620 — q2cbj1_9rhob like domain
Domain ID domain_id7zscC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id7zscC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id7zscC03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id7zscC04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id7zscD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id7zscD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id7zscD03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id7zscD04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin

8. Citations (1)

9. Files and Curves (10)