1b9l

7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE

Method: X-RAY DIFFRACTION D_max: 86.0 Å Quality: EXCELLENT

▼

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

PROTEIN (EPIMERASE)

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–120 Chain B； UniProt 1–120 Chain C； UniProt 1–120 Chain D； UniProt 1–120 Chain E； UniProt 1–120 Chain F； UniProt 1–120 Chain G； UniProt 1–120 Chain H； UniProt 1–120	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.90 Å R-free 0.259
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–120 Chain B； UniProt 1–120 Chain C； UniProt 1–120 Chain D； UniProt 1–120	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.90 Å R-free 0.259
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–120 Chain F； UniProt 1–120 Chain G； UniProt 1–120 Chain H； UniProt 1–120	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.90 Å R-free 0.259

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	FOLX_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–120； UniProt 1–120 Author chain B； PDBConstruct 1–120； UniProt 1–120 Author chain C； PDBConstruct 1–120； UniProt 1–120 Author chain D； PDBConstruct 1–120； UniProt 1–120 Author chain E； PDBConstruct 1–120； UniProt 1–120 Author chain F； PDBConstruct 1–120； UniProt 1–120 Author chain G； PDBConstruct 1–120； UniProt 1–120 Author chain H； PDBConstruct 1–120； UniProt 1–120

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b9l
Deposition date deposition_date	1999-02-11
Structure title title	7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE
Keywords keywords	EPIMERASE, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	30.69 Å
Radius of gyration Rg (electron density) rg_electron	29.37 Å
Forward intensity I(0) i0	202657000.00
Molecular weight molecular_weight	111460.0 kDa
Excluded volume excluded_volume	139450 Å³
Envelope volume envelope_volume	180010 Å³
Hydration-shell volume shell_volume	48772 Å³
Envelope diameter envelope_diameter	90.0 Å
Shell Rg shell_rg	38.42 Å
Envelope Rg envelope_rg	28.54 Å
Shape Rg shape_rg	29.39 Å
Total Rg total_rg	30.14 Å
Total atoms total_atoms	7872
Residues n_residues	952
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

▼

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

Maximum dimension Dmax dmax	86.0 Å
Rg (real space) rg_real	30.39 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.0270e+08
I(0) uncertainty (real space) i0_real_error	2.8200e+06
Rg (reciprocal space) rg_reciprocal	30.52 Å
I(0) (reciprocal space) i0_reciprocal	202700000.0000
Solution quality estimate total_estimate	0.9061
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	-0.053
Kurtosis Kurtosis kurtosis	-0.557
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	99280000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.943

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1b9la_
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

Domain ID domain_id	d1b9lb_
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

Domain ID domain_id	d1b9lc_
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

Domain ID domain_id	d1b9ld_
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

Domain ID domain_id	d1b9le_
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

Domain ID domain_id	d1b9lf_
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

Domain ID domain_id	d1b9lg_
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

Domain ID domain_id	d1b9lh_
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 (8 domains)

Domain ID domain_id	1b9lA00
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

Domain ID domain_id	1b9lB00
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

Domain ID domain_id	1b9lC00
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

Domain ID domain_id	1b9lD00
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

Domain ID domain_id	1b9lE00
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

Domain ID domain_id	1b9lF00
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

Domain ID domain_id	1b9lG00
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

Domain ID domain_id	1b9lH00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	69.680 Å
Unit-cell length b length_b	69.680 Å
Unit-cell length c length_c	239.720 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	32

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1880
R_free r_free	0.2590

Description description	PROTEIN (EPIMERASE)
Molecular weight formula_weight	14103.0 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	7872

7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE

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

PROTEIN (EPIMERASE)

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/b9/1b9l/1b9l.fit
pddf	/app/data/pr_computation/b9/1b9l/1b9l.pr.out
profile	/app/data/saxs_computation/b9/1b9l/1b9l.dat