SAXSdb — 1dl3

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

PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)

Thermotoga maritima

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 1–205	Mutation：A25Y,F55E,I101W	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；1 MM EDTA 0.5 MM DTT 0.1 M HEPES/NAOH 16.7 MG/ML PROTEIN 0.75 M POTASSIUM DIHYDROGEN PHOSPHATE 0.75 M SODIUM DIHYDROGEN PHOSPHATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.282
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–205	Mutation：A25Y,F55E,I101W	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；1 MM EDTA 0.5 MM DTT 0.1 M HEPES/NAOH 16.7 MG/ML PROTEIN 0.75 M POTASSIUM DIHYDROGEN PHOSPHATE 0.75 M SODIUM DIHYDROGEN PHOSPHATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.282

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 1DL3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LBM CRYSTAL STRUCTURE OF PHOSPHORIBOSYL ANTHRANILATE ISOMERASE (PRAI) IN COMPLEX WITH REDUCED 1-(O-CARBOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP) Deposited 2002-04-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–205（205 aa）	Not recorded	137 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；50 mM potassium phosphate , 2.1 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.228
1LBM CRYSTAL STRUCTURE OF PHOSPHORIBOSYL ANTHRANILATE ISOMERASE (PRAI) IN COMPLEX WITH REDUCED 1-(O-CARBOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP) Deposited 2002-04-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa）	Not recorded	137 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；50 mM potassium phosphate , 2.1 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.228
1NSJ CRYSTAL STRUCTURE OF PHOSPHORIBOSYL ANTHRANILATE ISOMERASE FROM THERMOTOGA MARITIMA Deposited 1996-09-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN 19.4 MG/ML IN 0.05 M POTASSIUM PHOSPHATE PH 7.5, 1MM EDTA, 0.4 MM DTT MIXED WITH RESERVOIR 1:1 CONTAINING 1.5-2.1 M AMMONIUM SULFATE, 10 MM COCL2, 0.1 M MES PH 6.5,	Resolution 2.00 Å R-free 0.243

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

View Construct and Data Evidence

UniProt name	TRPF_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 1–205 Author chain B； PDBConstruct 1–203； UniProt 1–205

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	1dl3
Deposition date deposition_date	1999-12-08
Structure title title	CRYSTAL STRUCTURE OF MUTUALLY GENERATED MONOMERS OF DIMERIC PHOSPHORIBOSYLANTRANILATE ISOMERASE FROM THERMOTOGA MARITIMA
Keywords keywords	ISOMERASE, OLIGOMERISATION, THERMOSTABILITY, THERMOTOGA MARITIMA, PROTEIN ENGINEERING, DIMER EVOLUTION; ISOMERASE
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	30.04 Å
Radius of gyration Rg (electron density) rg_electron	29.88 Å
Forward intensity I(0) i0	30213200.00
Molecular weight molecular_weight	43927.0 kDa
Excluded volume excluded_volume	55473 Å³
Envelope volume envelope_volume	69658 Å³
Hydration-shell volume shell_volume	20242 Å³
Envelope diameter envelope_diameter	99.9 Å
Shell Rg shell_rg	35.00 Å
Envelope Rg envelope_rg	29.64 Å
Shape Rg shape_rg	29.90 Å
Total Rg total_rg	30.36 Å
Total atoms total_atoms	3096
Residues n_residues	385
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	95.5 Å
Rg (real space) rg_real	30.32 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	3.0210e+07
I(0) uncertainty (real space) i0_real_error	4.7940e+05
Rg (reciprocal space) rg_reciprocal	30.21 Å
I(0) (reciprocal space) i0_reciprocal	30210000.0000
Solution quality estimate total_estimate	0.7710
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.821
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6502000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.616; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.551; Smooth: 0.621

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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	PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)
Molecular weight formula_weight	22973.3 kDa
EC 编号 ec_number	5.3.1.24
Mutation mutation	A25Y,F55E,I101W
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3128

MVRVKICGITNLEDALFSVESGADYVGFVFYPKSKRYISPEDARRISVELPVERVGVFVNEEPEKILDVASYVQLNAVQLHGEEPIELCRKIAERILVWKAVGVSNERDMERALNYREFPILLDTKTPEYGGSGKTFDWSLILPYRDRFRYLVLSGGLNPENVRSAIDVVRPFAVDVSSGVEAFPGKKDHDSIKMFIKNAKGL

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dl3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.4 — Tryptophan biosynthesis enzymes

Domain ID domain_id	d1dl3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.4 — Tryptophan biosynthesis enzymes

CATH v4.4 (2 domains)

Domain ID domain_id	1dl3A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1dl3B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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8. Citations (1)

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Unit-cell length a length_a	90.680 Å
Unit-cell length b length_b	94.650 Å
Unit-cell length c length_c	46.290 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1750
R_free r_free	0.2820

fit	/app/data/saxs_computation/dl/1dl3/1dl3.fit
pddf	/app/data/pr_computation/dl/1dl3/1dl3.pr.out
profile	/app/data/saxs_computation/dl/1dl3/1dl3.dat

CRYSTAL STRUCTURE OF MUTUALLY GENERATED MONOMERS OF DIMERIC PHOSPHORIBOSYLANTRANILATE ISOMERASE FROM THERMOTOGA MARITIMA

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

PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)

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