SAXSdb — 1cm7

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

PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–363 Chain B； UniProt 1–363	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；15 MG/ML PROTEIN IN 15% PEG 4K, 50 MM TRIS PH = 7.5, 0.35 M MGCL2	Resolution 2.06 Å R-free 0.245

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	LEU3_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–363； UniProt 1–363 Author chain B； PDBConstruct 1–363； UniProt 1–363

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	1cm7
Deposition date deposition_date	1999-05-17
Structure title title	3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA COLI
Keywords keywords	OXIDOREDUCTASE, DEHYDROGENASE, NAD-DEPENDANT ENZYME, LEUCINE BIOSYNTHETIC PATHWAY; OXIDOREDUCTASE
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	29.25 Å
Radius of gyration Rg (electron density) rg_electron	28.31 Å
Forward intensity I(0) i0	101133000.00
Molecular weight molecular_weight	78521.0 kDa
Excluded volume excluded_volume	97922 Å³
Envelope volume envelope_volume	119600 Å³
Hydration-shell volume shell_volume	35523 Å³
Envelope diameter envelope_diameter	95.9 Å
Shell Rg shell_rg	35.71 Å
Envelope Rg envelope_rg	28.10 Å
Shape Rg shape_rg	28.35 Å
Total Rg total_rg	28.89 Å
Total atoms total_atoms	5522
Residues n_residues	726
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	93.3 Å
Rg (real space) rg_real	29.24 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.0110e+08
I(0) uncertainty (real space) i0_real_error	1.6490e+06
Rg (reciprocal space) rg_reciprocal	29.25 Å
I(0) (reciprocal space) i0_reciprocal	101100000.0000
Solution quality estimate total_estimate	0.8898
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.6 Å
Skewness Skewness skewness	0.352
Kurtosis Kurtosis kurtosis	-0.384
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29580000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.886

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cm7a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

Domain ID domain_id	d1cm7b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

CATH v4.4 (2 domains)

Domain ID domain_id	1cm7A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

Domain ID domain_id	1cm7B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	55.800 Å
Unit-cell length b length_b	86.900 Å
Unit-cell length c length_c	83.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.060 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.1730
R_free r_free	0.2450

Description description	PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)
Molecular weight formula_weight	39559.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5753

3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA COLI

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

PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

fit	/app/data/saxs_computation/cm/1cm7/1cm7.fit
pddf	/app/data/pr_computation/cm/1cm7/1cm7.pr.out
profile	/app/data/saxs_computation/cm/1cm7/1cm7.dat