SAXSdb — 1ad1

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

DIHYDROPTEROATE SYNTHETASE

OrganismNot specified

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–267 Chain B； UniProt 2–267	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 experimental conditions	Resolution 2.20 Å R-free 0.218

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 1AD1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AD4 DIHYDROPTEROATE SYNTHETASE COMPLEXED WITH OH-CH2-PTERIN-PYROPHOSPHATE FROM STAPHYLOCOCCUS AUREUS Deposited 1997-02-20	Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different ligand/ion Different experimental conditions 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
6CLV Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–267（267 aa）	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
6CLV Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–267（267 aa）	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
6CLV Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–267（267 aa）	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
6CLV Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 2.30 Å R-free 0.210
6CLV Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–267（267 aa） Chain D 1–267（267 aa）	Mutation：F17L, E208K 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
6CLV Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure Deposited 2018-03-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–267（267 aa） Chain C 1–267（267 aa）	Mutation：F17L, E208K 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

3 other PDB entries and 13 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 1–266； UniProt 2–267 Author chain B； PDBConstruct 1–266； UniProt 2–267

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	1ad1
Deposition date deposition_date	1997-02-19
Structure title title	DIHYDROPTEROATE SYNTHETASE (APO FORM) FROM STAPHYLOCOCCUS AUREUS
Keywords keywords	SYNTHETASE, TRANSFERASE, DIHYDROPTEROATE SYNTHETASE, DHPS, APO FORM, COMPLEX WITH OH-CH2-PTERIN-PYROPHOSPHATE; TRANSFERASE
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	26.87 Å
Radius of gyration Rg (electron density) rg_electron	26.28 Å
Forward intensity I(0) i0	54418300.00
Molecular weight molecular_weight	57029.0 kDa
Excluded volume excluded_volume	71349 Å³
Envelope volume envelope_volume	85626 Å³
Hydration-shell volume shell_volume	28020 Å³
Envelope diameter envelope_diameter	91.7 Å
Shell Rg shell_rg	32.74 Å
Envelope Rg envelope_rg	26.35 Å
Shape Rg shape_rg	26.30 Å
Total Rg total_rg	26.91 Å
Total atoms total_atoms	3994
Residues n_residues	515
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	87.2 Å
Rg (real space) rg_real	26.97 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	5.4420e+07
I(0) uncertainty (real space) i0_real_error	7.8960e+05
Rg (reciprocal space) rg_reciprocal	26.94 Å
I(0) (reciprocal space) i0_reciprocal	54420000.0000
Solution quality estimate total_estimate	0.8035
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.449
Kurtosis Kurtosis kurtosis	-0.358
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13610000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.000

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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	DIHYDROPTEROATE SYNTHETASE
Molecular weight formula_weight	29402.5 kDa
EC 编号 ec_number	2.5.1.15
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4395

TKTKIMGILNVTPDSFSDGGKFNNVESAVTRVKAMMDEGADIIDVGGVSTRPGHEMITVEEELNRVLPVVEAIVGFDVKISVDTFRSEVAEACLKLGVDIINDQWAGLYDHRMFQVVAKYDAEIVLMHNGNGNRDEPVVEEMLTSLLAQAHQAKIAGIPSNKIWLDPGIGFAKTRNEEAEVMARLDELVATEYPVLLATSRKRFTKEMMGYDTTPVERDEVTAATTAYGIMKGVRAVRVHNVELNAKLAKGIDFLKENENARHNFS

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 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	401

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ad1a_
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	d1ad1b_
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 (2 domains)

Domain ID domain_id	1ad1A00
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	1ad1B00
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	64.470 Å
Unit-cell length b length_b	42.190 Å
Unit-cell length c length_c	101.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	13.500 Å
R factor r_factor	0.1590
R_work r_work	0.1590
R_free r_free	0.2180

fit	/app/data/saxs_computation/ad/1ad1/1ad1.fit
pddf	/app/data/pr_computation/ad/1ad1/1ad1.pr.out
profile	/app/data/saxs_computation/ad/1ad1/1ad1.dat

DIHYDROPTEROATE SYNTHETASE (APO FORM) FROM STAPHYLOCOCCUS AUREUS

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

DIHYDROPTEROATE SYNTHETASE

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