SAXSdb — 1dk4

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

INOSITOL MONOPHOSPHATASE

Methanocaldococcus jannaschii

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 1–252 Chain B； UniProt 1–252	Not recorded	ZN ZINC ION × 6 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 8000, calcium chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.331

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 1DK4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G0H CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE-FRUCTOSE 1,6 BISPHOSPHATASE Deposited 2000-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–252（252 aa） Chain B 1–252（252 aa）	Not recorded	CA CALCIUM ION × 4 IPD D-MYO-INOSITOL-1-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 8000, sodium chloride, calcium chloride, TRIS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.30 Å R-free 0.279
1G0I CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE-FRUCTOSE 1,6 BISPHOSPHATASE Deposited 2000-10-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–252（252 aa） Chain B 1–252（252 aa）	Not recorded	MN MANGANESE (II) ION × 6 PO4 PHOSPHATE ION × 2 INS 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 8000, sodium chloride, manganese chloride, TRIS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.339

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

View Construct and Data Evidence

UniProt name	SUHB_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–252； UniProt 1–252 Author chain B； PDBConstruct 1–252； UniProt 1–252

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	1dk4
Deposition date deposition_date	1999-12-06
Structure title title	CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE
Keywords keywords	HOMODIMER, COMPLEXED WITH ZN AND PI, HYDROLASE; HYDROLASE
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	23.98 Å
Radius of gyration Rg (electron density) rg_electron	23.02 Å
Forward intensity I(0) i0	50617900.00
Molecular weight molecular_weight	57730.0 kDa
Excluded volume excluded_volume	73154 Å³
Envelope volume envelope_volume	82656 Å³
Hydration-shell volume shell_volume	29220 Å³
Envelope diameter envelope_diameter	83.5 Å
Shell Rg shell_rg	30.74 Å
Envelope Rg envelope_rg	23.26 Å
Shape Rg shape_rg	23.03 Å
Total Rg total_rg	23.88 Å
Total atoms total_atoms	4052
Residues n_residues	504
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	80.7 Å
Rg (real space) rg_real	23.91 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	5.0620e+07
I(0) uncertainty (real space) i0_real_error	8.0650e+05
Rg (reciprocal space) rg_reciprocal	23.93 Å
I(0) (reciprocal space) i0_reciprocal	50620000.0000
Solution quality estimate total_estimate	0.7939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15590000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.783; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; 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	INOSITOL MONOPHOSPHATASE
Molecular weight formula_weight	28611.8 kDa
EC 编号 ec_number	3.1.3.25
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	4106

MKWDEIGKNIAKEIEKEILPYFGRKDKSYVVGTSPSGDETEIFDKISEDIALKYLKSLNVNIVSEELGVIDNSSEWTVVIDPIDGSFNFINGIPFFAFCFGVFKNNEPYYGLTYEFLTKSFYEAYKGKGAYLNGRKIKVKDFNPNNIVISYYPSKKIDLEKLRNKVKRVRIFGAFGLEMCYVAKGTLDAVFDVRPKVRAVDIASSYIICKEAGALITDENGDELKFDLNATDRLNIIVANSKEMLDIILDLL

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI Class编号 ncbi_taxonomy_id	2190
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	54

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dk4a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d1dk4b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1dk4A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1dk4A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1dk4B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1dk4B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

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8. Citations (1)

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Unit-cell length a length_a	68.870 Å
Unit-cell length b length_b	78.430 Å
Unit-cell length c length_c	129.720 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2430
R_work r_work	0.2420
R_free r_free	0.3310

fit	/app/data/saxs_computation/dk/1dk4/1dk4.fit
pddf	/app/data/pr_computation/dk/1dk4/1dk4.pr.out
profile	/app/data/saxs_computation/dk/1dk4/1dk4.dat

CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE

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

INOSITOL MONOPHOSPHATASE

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