SAXSdb — 1dhn

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

7,8-DIHYDRONEOPTERIN ALDOLASE

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 homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–121	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 1.65 Å R-free 0.252

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 1DHN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RRI DHNA complex with 3-(5-amino-7-hydroxy-[1,2,3] triazolo [4,5-d]pyrimidin-2-yl)-benzoic acid Deposited 2003-12-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	A45 3-(5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-BENZOIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M Ammonium Acetate, 0.1M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.316
1RRW DHNA complexed with 9-methylguanine Deposited 2003-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	9MG 9-METHYLGUANINE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M Ammonium Acetate, 0.1M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.21 Å R-free 0.356
1RRY DHNA complexed with 2-amino-4-hydroxy-5-carboxyethylpyrimidine Deposited 2003-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	204 2-AMINO-4-HYDROXYPYRIMIDINE-5-CARBOXYLIC ACID ETHYL ESTER × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2 M Ammonium Acetate, 0.1 M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.70 Å R-free 0.305
1RS2 DHNA complex with 8-Amino-1,3-dimethyl-3,7-dihydropurine-2,6-dione Deposited 2003-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	209 8-AMINO-1,3-DIMETHYL-3,7-DIHYDROPURINE-2,6-DIONE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M Ammonium Acetate, 0.1M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.31 Å R-free 0.311
1RS4 DHNA, 7,8-Dihydroneopterin Aldolase complexed with 3-(5-Amino-7-hydroxy-[1,2,3]triazolo[4,5-d]pyrimidin-2-yl)-N-(3,5-dichlorobenzyl)-benzamide Deposited 2003-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	45P 3-(5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-N-(3,5-DICHLOROBENZYL)-BENZAMIDE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；0.2M Ammonium Acetate, 0.1M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.295
1RSD DHNA complex with 3-(5-Amino-7-hydroxy-[1,2,3]triazolo[4,5-d]pyrimidin-2-yl)-N-[2-(2-hydroxymethyl-phenylsulfanyl)-benzyl]-benzamide Deposited 2003-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	PSB 3-(5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-N-[2-(2-(HYDROXYMETHYL-PHENYLSULFANYL)-BENZYL]-BENZAMIDE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M Ammonium Acetate, 0.1M tri-sodium citrate, 30% MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.293
1RSI DHNA complex with 2-Amino-5-bromo-3-hydroxy-6-phenylpyrimidine Deposited 2003-12-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	977 2-AMINO-5-BROMO-6-PHENYLPYRIMIDIN-4-OL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2 M Ammonium Acetate, 0.1 M tri-sodium citrate, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 5.6	Resolution 2.20 Å R-free 0.339
1U68 DHNA 7,8 DIHYDRONEOPTERIN COMPLEX Deposited 2004-07-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	NPR 2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M AMMONIUM ACETATE, 0.1M TRI-SODIUM CITRATE, 30% MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.40 Å R-free 0.368
2DHN COMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 2.2 A RESOLUTION Deposited 1998-03-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	PH2 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.6；pH 6.6	Resolution 2.20 Å R-free 0.298
2NM2 Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2R)-neopterin at 1.50 Angstrom resolution Deposited 2006-10-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa） Chain B 1–121（121 aa） Chain C 1–121（121 aa） Chain D 1–121（121 aa）	Not recorded	NEU L-NEOPTERIN × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；292 K；0.8M Sodium-potassium tartrate, 0.1M HEPES, 10mM Tris-HCL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.70 Å R-free 0.262
2NM3 Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2S)-monapterin at 1.68 angstrom resolution Deposited 2006-10-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–121（121 aa）	Not recorded	ACT ACETATE ION × 8 MPU D-MONAPTERIN × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；292 K；1.4M Sodium acetate, 0.2M Imidazole, 0.1M Sodium cacodylate, 10mM Tris-HCL, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.68 Å R-free 0.262

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FOLB_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 1–121

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	1dhn
Deposition date deposition_date	1998-03-31
Structure title title	1.65 ANGSTROM RESOLUTION STRUCTURE OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS
Keywords keywords	PTERIN BINDING, FOLATE BIOSYNTHESIS, ANTIBIOTIC TARGET, BETA-BARREL; PTERIN BINDING
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	16.94 Å
Radius of gyration Rg (electron density) rg_electron	15.83 Å
Forward intensity I(0) i0	3806610.00
Molecular weight molecular_weight	13747.0 kDa
Excluded volume excluded_volume	17177 Å³
Envelope volume envelope_volume	20365 Å³
Hydration-shell volume shell_volume	11746 Å³
Envelope diameter envelope_diameter	59.0 Å
Shell Rg shell_rg	20.57 Å
Envelope Rg envelope_rg	16.36 Å
Shape Rg shape_rg	15.84 Å
Total Rg total_rg	16.73 Å
Total atoms total_atoms	967
Residues n_residues	121
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	60.5 Å
Rg (real space) rg_real	17.03 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	3.8070e+06
I(0) uncertainty (real space) i0_real_error	4.6020e+04
Rg (reciprocal space) rg_reciprocal	17.02 Å
I(0) (reciprocal space) i0_reciprocal	3807000.0000
Solution quality estimate total_estimate	0.6774
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.3 Å
Skewness Skewness skewness	0.531
Kurtosis Kurtosis kurtosis	-0.048
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	712900.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 0.322; Positv: 1.000; Valcen: 0.838; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dhna_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.3 — DHN aldolase/epimerase

CATH v4.4 (1 domains)

Domain ID domain_id	1dhnA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1130 — GTP Cyclohydrolase I, domain 2
Homologous superfamily homologous superfamily	10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	61.300 Å
Unit-cell length b length_b	61.300 Å
Unit-cell length c length_c	124.200 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	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2520

Description description	7,8-DIHYDRONEOPTERIN ALDOLASE
Molecular weight formula_weight	13769.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1089

1.65 ANGSTROM RESOLUTION STRUCTURE OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS

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

7,8-DIHYDRONEOPTERIN ALDOLASE

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

fit	/app/data/saxs_computation/dh/1dhn/1dhn.fit
pddf	/app/data/pr_computation/dh/1dhn/1dhn.pr.out
profile	/app/data/saxs_computation/dh/1dhn/1dhn.dat