6hps

Near-infrared dual bioluminescence imaging in vivo using infra-luciferin

Method: X-RAY DIFFRACTION Dmax: 117.7 Å Quality: GOOD

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

Luciferin 4-monooxygenase

Photinus pyralis

UniProt P08659

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 4–546 Not recorded GKH [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;278 K;150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000 Resolution 3.10 Å R-free 0.333
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 4–546 Not recorded GKH [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[[2-[(~{E})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)ethenyl]-1,3-thiazol-4-yl]carbonyl]sulfamate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;278 K;150 mM ammonium sulfate, 50 mM HEPES pH 7.0, 2% PEG 1000 Resolution 3.10 Å R-free 0.333

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.

17 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LUCI_PHOPY
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–543; UniProt 4–546 Author chain B; PDBConstruct 1–543; UniProt 4–546

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 6hps

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6hps
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6hps
Deposition date deposition_date2018-09-21
Structure title titleNear-infrared dual bioluminescence imaging in vivo using infra-luciferin
Keywords keywords;near-infrared Bioluminescence imaging, P. pyralis luciferase, ANL SUPERFAMILY, LIGASE, ADENYLATING ENZYMES, LUCIFERASE, DOMAIN ALTERNATION, FLUORESCENT PROTEIN ;; FLUORESCENT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.95
Radius of gyration Rg (electron density) rg_electron35.50
Forward intensity I(0) i0208006000.00
Molecular weight molecular_weight120740.0 kDa
Excluded volume excluded_volume152930 ų
Envelope volume envelope_volume194890 ų
Hydration-shell volume shell_volume45598 ų
Envelope diameter envelope_diameter121.5
Shell Rg shell_rg41.96
Envelope Rg envelope_rg35.04
Shape Rg shape_rg35.50
Total Rg total_rg35.96
Total atoms total_atoms8510
Residues n_residues1082
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 dmax117.7
Rg (real space) rg_real35.98
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real2.0800e+08
I(0) uncertainty (real space) i0_real_error3.8320e+06
Rg (reciprocal space) rg_reciprocal35.96
I(0) (reciprocal space) i0_reciprocal208000000.0000
Solution quality estimate total_estimate0.8869
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.8
Skewness Skewness skewness0.315
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha68170000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.849

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6hpsa_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamilye.23.1 — Acetyl-CoA synthetase-like
Family Family familye.23.1.1 — Acetyl-CoA synthetase-like
Domain ID domain_idd6hpsb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamilye.23.1 — Acetyl-CoA synthetase-like
Family Family familye.23.1.1 — Acetyl-CoA synthetase-like

CATH v4.4 (2 domains)

Domain ID domain_id6hpsA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily30 — ANL, C-terminal domain
Domain ID domain_id6hpsB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily30 — ANL, C-terminal domain

8. Citations (1)

9. Files and Curves (10)