SAXSdb — 6clv

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

Dihydropteroate synthase

Staphylococcus aureus

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 1–267	Mutation：F17L, E208K	6MB 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 2.30 Å R-free 0.210
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–267	Mutation：F17L, E208K	6MB 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 2.30 Å R-free 0.210
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–267	Mutation：F17L, E208K	6MB 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 2.30 Å R-free 0.210
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–267	Mutation：F17L, E208K	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 2.30 Å R-free 0.210
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–267 Chain D； UniProt 1–267	Mutation：F17L, E208K	6MB 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 2.30 Å R-free 0.210
6	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–267 Chain C； UniProt 1–267	Mutation：F17L, E208K	6MB 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 2.30 Å R-free 0.210

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 6CLV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AD1 DIHYDROPTEROATE SYNTHETASE (APO FORM) FROM STAPHYLOCOCCUS AUREUS Deposited 1997-02-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–267（266 aa） Chain B 2–267（266 aa）	Not recorded	K POTASSIUM ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.218
1AD4 DIHYDROPTEROATE SYNTHETASE COMPLEXED WITH OH-CH2-PTERIN-PYROPHOSPHATE FROM STAPHYLOCOCCUS AUREUS Deposited 1997-02-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–267（266 aa） Chain B 2–267（266 aa）	Not recorded	MN MANGANESE (II) ION × 3 K POTASSIUM ION × 2 HH2 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
6CLU Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–267（267 aa）	Mutation：F17L, E208K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 1.95 Å R-free 0.204
6CLU Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–267（267 aa）	Mutation：F17L, E208K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 1.95 Å R-free 0.204
6CLU Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–267（267 aa）	Mutation：F17L, E208K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 1.95 Å R-free 0.204
6CLU Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–267（267 aa）	Mutation：F17L, E208K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 1.95 Å R-free 0.204
6CLU Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–267（267 aa） Chain B 1–267（267 aa）	Mutation：F17L, E208K Mutation：F17L, E208K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 1.95 Å R-free 0.204
6CLU Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–267（267 aa） Chain D 1–267（267 aa）	Mutation：F17L, E208K Mutation：F17L, E208K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium Nitrate, and 20% PEG 3350	Resolution 1.95 Å R-free 0.204

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHPS_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–291； UniProt 1–267 Author chain B； PDBConstruct 25–291； UniProt 1–267 Author chain C； PDBConstruct 25–291； UniProt 1–267 Author chain D； PDBConstruct 25–291； UniProt 1–267

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	6clv
Deposition date deposition_date	2018-03-02
Structure title title	Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure
Keywords keywords	antibiotic resistance mutations, sulfonamide resistance, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
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	32.95 Å
Radius of gyration Rg (electron density) rg_electron	32.14 Å
Forward intensity I(0) i0	179381000.00
Molecular weight molecular_weight	106090.0 kDa
Excluded volume excluded_volume	132610 Å³
Envelope volume envelope_volume	169390 Å³
Hydration-shell volume shell_volume	43107 Å³
Envelope diameter envelope_diameter	101.2 Å
Shell Rg shell_rg	39.70 Å
Envelope Rg envelope_rg	31.68 Å
Shape Rg shape_rg	32.17 Å
Total Rg total_rg	32.65 Å
Total atoms total_atoms	7443
Residues n_residues	1002
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	98.1 Å
Rg (real space) rg_real	32.71 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.7940e+08
I(0) uncertainty (real space) i0_real_error	2.2840e+06
Rg (reciprocal space) rg_reciprocal	32.82 Å
I(0) (reciprocal space) i0_reciprocal	179400000.0000
Solution quality estimate total_estimate	0.9110
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.0 Å
Skewness Skewness skewness	0.004
Kurtosis Kurtosis kurtosis	-0.748
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	66800000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Dihydropteroate synthase
Molecular weight formula_weight	32406.9 kDa
EC 编号 ec_number	2.5.1.15
Mutation mutation	F17L, E208K
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7542

MGHHHHHHHHHHSSGHIEGRHMLEMTKTKIMGILNVTPDSLSDGGKFNNVESAVTRVKAMMDEGADIIDVGGVSTRPGHEMITVEEELNRVLPVVEAIVGFDVKISVDTFRSEVAEACLKLGVDIINDQWAGLYDHRMFQVVAKYDAEIVLMHNGNGNRDEPVVEEMLTSLLAQAHQAKIAGIPSNKIWLDPGIGFAKTRNEEAEVMARLDELVATEYPVLLATSRKRFTKKMMGYDTTPVERDEVTAATTAYGIMKGVRAVRVHNVELNAKLAKGIDFLKENENARHNFS

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide
Molecular weight formula_weight	442.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6clva_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.1 — Dihydropteroate synthetase

Domain ID domain_id	d6clvb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.1 — Dihydropteroate synthetase

Domain ID domain_id	d6clvc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.1 — Dihydropteroate synthetase

Domain ID domain_id	d6clvd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.1 — Dihydropteroate synthetase

CATH v4.4 (4 domains)

Domain ID domain_id	6clvA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	6clvB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	6clvC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	6clvD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

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8. Citations (1)

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Unit-cell length a length_a	79.750 Å
Unit-cell length b length_b	79.750 Å
Unit-cell length c length_c	175.400 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	16

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	47.432 Å
R factor r_factor	0.2119
R_work r_work	0.1907
R_free r_free	0.2099

fit	/app/data/saxs_computation/cl/6clv/6clv.fit
pddf	/app/data/pr_computation/cl/6clv/6clv.pr.out
profile	/app/data/saxs_computation/cl/6clv/6clv.dat

Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure

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

Dihydropteroate synthase

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