SAXSdb — 1di6

▼

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

MOLYBDENUM COFACTOR BIOSYNTHETIC ENZYME

Escherichia coli

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–195	Mutation：N2A	SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 9；295 K；2.0 - 2.1 M AMMONIUM SULFATE, 0.1 M BICINE pH 9.0, VAPOR DIFFUSION, temperature 295K	Resolution 1.45 Å R-free 0.213

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 1DI6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DI7 1.60 ANGSTROM CRYSTAL STRUCTURE OF THE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN MOGA FROM ESCHERICHIA COLI Deposited 1999-11-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–195（195 aa）	Mutation：N2A	SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；295 K；2.3 - 2.4 M AMMONIUM SULFATE, 0.1 M BICINE pH 9.0, VAPOR DIFFUSION, temperature 295K	Resolution 1.60 Å R-free 0.226

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MOG_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–195； UniProt 1–195

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1di6
Deposition date deposition_date	1999-11-29
Structure title title	1.45 A CRYSTAL STRUCTURE OF THE MOLYBDENUMM COFACTOR BIOSYNTHESIS PROTEIN MOGA FROM ESCHERICHIA COLI
Keywords keywords	MOLYBDENUM COFACTOR, MOCO, MOCO BIOSYNTHESIS, MOGA, GEPHYRIN, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.07 Å
Radius of gyration Rg (electron density) rg_electron	15.62 Å
Forward intensity I(0) i0	7493060.00
Molecular weight molecular_weight	19882.0 kDa
Excluded volume excluded_volume	24881 Å³
Envelope volume envelope_volume	28347 Å³
Hydration-shell volume shell_volume	15194 Å³
Envelope diameter envelope_diameter	53.9 Å
Shell Rg shell_rg	21.65 Å
Envelope Rg envelope_rg	15.93 Å
Shape Rg shape_rg	15.62 Å
Total Rg total_rg	16.68 Å
Total atoms total_atoms	1392
Residues n_residues	183
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	54.0 Å
Rg (real space) rg_real	16.95 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	7.4930e+06
I(0) uncertainty (real space) i0_real_error	7.9820e+04
Rg (reciprocal space) rg_reciprocal	16.97 Å
I(0) (reciprocal space) i0_reciprocal	7493000.0000
Solution quality estimate total_estimate	0.8864
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.109
Kurtosis Kurtosis kurtosis	-0.361
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1721000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.980

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	MOLYBDENUM COFACTOR BIOSYNTHETIC ENZYME
Molecular weight formula_weight	21200.3 kDa
Mutation mutation	N2A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1554

MATLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDEQAIIEQTLCELVDEMSCHLVLTTGGTGPARRDVTPDATLAVADREMPGFGEQMRQISLHFVPTAILSRQVGVIRKQALILNLPGQPKSIKETLEGVKDAEGNVVVHGIFASVPYCIQLLEGPYVETAPEVVAAFRPKSARRDVSE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
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	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	128

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1di6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.57 — Molybdenum cofactor biosynthesis proteins
Superfamily Superfamily superfamily	c.57.1 — Molybdenum cofactor biosynthesis proteins
Family Family family	c.57.1.1 — MogA-like

CATH v4.4 (1 domains)

Domain ID domain_id	1di6A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	980 — Molybdenum Cofactor Biosythetic Enzyme; Chain A
Homologous superfamily homologous superfamily	10 — MoaB/Mog-like domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	65.300 Å
Unit-cell length b length_b	65.300 Å
Unit-cell length c length_c	65.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1870
R_free r_free	0.2130

fit	/app/data/saxs_computation/di/1di6/1di6.fit
pddf	/app/data/pr_computation/di/1di6/1di6.pr.out
profile	/app/data/saxs_computation/di/1di6/1di6.dat

1.45 A CRYSTAL STRUCTURE OF THE MOLYBDENUMM COFACTOR BIOSYNTHESIS PROTEIN MOGA FROM ESCHERICHIA COLI

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

MOLYBDENUM COFACTOR BIOSYNTHETIC ENZYME

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