9y43

3-hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.

Method: X-RAY DIFFRACTION Dmax: 114.6 Å Quality: GOOD

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

3-hydroxypropionate--CoA ligase [ADP-forming]

Nitrosopumilus maritimus SCM1

UniProt A9A2G6

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 1–705 Chain B; UniProt 1–705 Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 3OH 3-HYDROXY-PROPANOIC ACID × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;200 mM Magnesium chloride hexahydrate, 100 mM Tris pH 8.5, 7% (v/v) PEG 6000 Resolution 2.80 Å R-free 0.254

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name HPCAL_NITMS
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–705; UniProt 1–705 Author chain B; PDBConstruct 1–705; UniProt 1–705

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 9y43

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y43
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y43
Deposition date deposition_date2025-09-02
Structure title title3-hydroxypropionyl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.
Keywords keywordsCarbon Fixation, HP/HB cycle, ACD, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.06
Radius of gyration Rg (electron density) rg_electron35.74
Forward intensity I(0) i0326711000.00
Molecular weight molecular_weight151510.0 kDa
Excluded volume excluded_volume192180 ų
Envelope volume envelope_volume241010 ų
Hydration-shell volume shell_volume55061 ų
Envelope diameter envelope_diameter123.5
Shell Rg shell_rg42.89
Envelope Rg envelope_rg35.64
Shape Rg shape_rg35.73
Total Rg total_rg36.27
Total atoms total_atoms10636
Residues n_residues1394
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 dmax114.6
Rg (real space) rg_real35.95
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real3.2670e+08
I(0) uncertainty (real space) i0_real_error5.4010e+06
Rg (reciprocal space) rg_reciprocal36.02
I(0) (reciprocal space) i0_reciprocal326700000.0000
Solution quality estimate total_estimate0.8990
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.9
Skewness Skewness skewness0.230
Kurtosis Kurtosis kurtosis-0.415
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha71320000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.902

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)