7zbd

HaloTag with TRaQ-G ligand

Method: X-RAY DIFFRACTION Dmax: 90.1 Å Quality: GOOD

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

Haloalkane dehalogenase

Rhodococcus sp.

UniProt P0A3G3

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 1–290 Not recorded GOL GLYCEROL × 1 ILQ (10R)-7-azanyl-N-[2-[2-(6-chloranylhexoxy)ethoxy]ethyl]-2'-cyano-5,5-dimethyl-3-(methylamino)-1'-oxidanylidene-spiro[benzo[b][1]benzosiline-10,3'-isoindole]-5'-carboxamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;20% v/v PEG 6000, 10% ethylene glycol, 0.1M magnesium chloride hexahydrate and 0.1M MES Resolution 1.68 Å R-free 0.222
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–290 Not recorded GOL GLYCEROL × 1 CL CHLORIDE ION × 1 ILU [7-azanyl-10-[5-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]-2-(cyanocarbamoyl)phenyl]-5,5-dimethyl-benzo[b][1]benzosilin-3-ylidene]-methyl-azanium × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;20% v/v PEG 6000, 10% ethylene glycol, 0.1M magnesium chloride hexahydrate and 0.1M MES Resolution 1.68 Å R-free 0.222

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.

41 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DHAA_RHOSO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–290; UniProt 1–290 Author chain B; PDBConstruct 1–290; UniProt 1–290

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 7zbd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7zbd
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7zbd
Deposition date deposition_date2022-03-23
Structure title titleHaloTag with TRaQ-G ligand
Keywords keywordsHaloTag, haloalkane dehalogenase, silicon rhodamine, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.94
Radius of gyration Rg (electron density) rg_electron27.37
Forward intensity I(0) i067964500.00
Molecular weight molecular_weight67464.0 kDa
Excluded volume excluded_volume85488 ų
Envelope volume envelope_volume96530 ų
Hydration-shell volume shell_volume30052 ų
Envelope diameter envelope_diameter94.8
Shell Rg shell_rg34.00
Envelope Rg envelope_rg27.34
Shape Rg shape_rg27.37
Total Rg total_rg28.09
Total atoms total_atoms4878
Residues n_residues582
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 dmax90.1
Rg (real space) rg_real28.06
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real6.7960e+07
I(0) uncertainty (real space) i0_real_error1.0420e+06
Rg (reciprocal space) rg_reciprocal28.02
I(0) (reciprocal space) i0_reciprocal67960000.0000
Solution quality estimate total_estimate0.8708
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.5
Skewness Skewness skewness0.437
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58610000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.870

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7zbdA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id7zbdB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain

8. Citations (4)

9. Files and Curves (10)