SAXSdb — 3flb

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

RifR

Amycolatopsis mediterranei

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	Mutation：S94A	CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 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 0.239

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.

Other PDB	Difference from Current Entry 3FLB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FLA RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 1 Deposited 2008-12-18	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–259（259 aa）	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
3FLA RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 1 Deposited 2008-12-18	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–259（259 aa）	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
9PC6 Antibody (1B2) Bound Crosslinked Rifamycin Synthetase Module 1 with a C-terminal Type II Thioesterase Deposited 2025-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 2–259（258 aa） Chain B 2–259（258 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å

2 other PDB entries and 3 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3flb
Deposition date deposition_date	2008-12-18
Structure title title	RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 2
Keywords keywords	alpha-beta hydrolase thioesterase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.07 Å
Radius of gyration Rg (electron density) rg_electron	16.64 Å
Forward intensity I(0) i0	13381100.00
Molecular weight molecular_weight	26993.0 kDa
Excluded volume excluded_volume	33657 Å³
Envelope volume envelope_volume	37286 Å³
Hydration-shell volume shell_volume	18276 Å³
Envelope diameter envelope_diameter	56.5 Å
Shell Rg shell_rg	23.29 Å
Envelope Rg envelope_rg	16.88 Å
Shape Rg shape_rg	16.63 Å
Total Rg total_rg	17.65 Å
Total atoms total_atoms	1901
Residues n_residues	245
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	57.0 Å
Rg (real space) rg_real	17.90 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.3380e+07
I(0) uncertainty (real space) i0_real_error	1.7050e+05
Rg (reciprocal space) rg_reciprocal	17.92 Å
I(0) (reciprocal space) i0_reciprocal	13380000.0000
Solution quality estimate total_estimate	0.8846
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.051
Kurtosis Kurtosis kurtosis	-0.456
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5592000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RifR
Molecular weight formula_weight	29262.3 kDa
EC 编号 ec_number	3.1.2.-
Mutation mutation	S94A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2110

MHRPEAEKWLRRFERAPDARARLVCLPHAGGSASFFFPLAKALAPAVEVLAVQYPGRQDRRHEPPVDSIGGLTNRLLEVLRPFGDRPLALFGHAMGAIIGYELALRMPEAGLPAPVHLFASGRRAPSRYRDDDVRGASDERLVAELRKLGGSDAAMLADPELLAMVLPAIRSDYRAVETYRHEPGRRVDCPVTVFTGDHDPRVSVGEARAWEEHTTGPADLRVLPGGHFFLVDQAAPMIATMTEKLAGPALTGSTGGNSLEHHHHHH

来源 Source

来源生物 organism	Amycolatopsis mediterranei
通用名 common_name	Nocardia mediterranei
NCBI Class编号 ncbi_taxonomy_id	33910
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3flbA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	38.938 Å
Unit-cell length b length_b	62.497 Å
Unit-cell length c length_c	82.467 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	49.810 Å
R factor r_factor	0.1886
R_work r_work	0.1859
R_free r_free	0.2386

fit	/app/data/saxs_computation/fl/3flb/3flb.fit
pddf	/app/data/pr_computation/fl/3flb/3flb.pr.out
profile	/app/data/saxs_computation/fl/3flb/3flb.dat

RifR - Type II thioesterase from Rifamycin NRPS/PKS biosynthetic pathway - Form 2

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

RifR

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction