3fla

RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 1

Method: X-RAY DIFFRACTION Dmax: 82.2 Å Quality: GOOD

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

RifR

Amycolatopsis mediterranei

UniProt Q7BUF9

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 1–259 Non-standard monomer:Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;100 mM HEPES pH 7.0, 12% PEG 8000, 50 mM CaCl2, 2 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.80 Å R-free 0.202
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–259 Non-standard monomer:Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;100 mM HEPES pH 7.0, 12% PEG 8000, 50 mM CaCl2, 2 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.80 Å R-free 0.202

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q7BUF9_AMYMD
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–259; UniProt 1–259 Author chain B; PDBConstruct 1–259; UniProt 1–259

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 3fla

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fla
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fla
Deposition date deposition_date2008-12-18
Structure title titleRifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 1
Keywords keywordsalpha-beta hydrolase thioesterase, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.75
Radius of gyration Rg (electron density) rg_electron26.03
Forward intensity I(0) i053024900.00
Molecular weight molecular_weight54680.0 kDa
Excluded volume excluded_volume67515 ų
Envelope volume envelope_volume81648 ų
Hydration-shell volume shell_volume26559 ų
Envelope diameter envelope_diameter84.2
Shell Rg shell_rg32.91
Envelope Rg envelope_rg25.91
Shape Rg shape_rg26.05
Total Rg total_rg26.72
Total atoms total_atoms3812
Residues n_residues480
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 dmax82.2
Rg (real space) rg_real26.80
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real5.3020e+07
I(0) uncertainty (real space) i0_real_error8.1150e+05
Rg (reciprocal space) rg_reciprocal26.79
I(0) (reciprocal space) i0_reciprocal53020000.0000
Solution quality estimate total_estimate0.8929
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.9
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.620
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12380000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.867

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3flaA00
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_id3flaB00
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 (1)

9. Files and Curves (10)