SAXSdb — 2dk9

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

NEDD9-interacting protein with calponin homology and LIM domains

Homo sapiens

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 506–614	Fragment：Calponin Homology domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；293 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer, 50mM NaCl；Pressure 1 NMR sample composition：1.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：1.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：1.5mM MICAL_1 CH U-15N,13C; 50mM phosphate buffer, 50mM NaCl; 100% D2O \| 100% D2O NMR sample composition：1.5mM MICAL_1 CH U-15N; 50mM phosphate buffer, 50mM NaCl; 17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O \| 17 mg/mL Pf1 filamentous phage; 90% H2O, 10% D2O	Resolution not provided

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 2DK9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WYL Solution structure of the CH domain of human NEDD9 interacting protein with calponin homology and LIM domains Deposited 2005-02-15	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 510–612（103 aa） Fragment：CH domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.22mM CH domain U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2CO8 Solution structures of the LIM domain of human NEDD9 interacting protein with calponin homology and LIM domains Deposited 2005-05-17	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 687–755（69 aa） Fragment：LIM domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM LIM domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZnCl2; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
5LE0 MICAL1 Cterminal domain Deposited 2016-06-29	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 918–1067（150 aa） Fragment：UNP residues 918-1067	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；EG	Resolution 3.30 Å R-free 0.306
5LPN Structure of human Rab10 in complex with the bMERB domain of Mical-1 Deposited 2016-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 918–1067（150 aa） Fragment：UNP residues 918-1067	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；6%-10% PEG8000 0.1M Imidazole	Resolution 2.80 Å R-free 0.287
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 799–822（24 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
6KU0 Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM Deposited 2019-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 799–822（24 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；1% w/v Tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3350	Resolution 1.60 Å R-free 0.199
8HLO Crystal structure of ASAP1-SH3 and MICAL1-PRM complex Deposited 2022-11-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 828–836（9 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；289.15 K；0.1M HEPES, pH 7.5, 1.4M Sodium citrate tribasic dihydrate	Resolution 1.17 Å R-free 0.142
8Y6K Cryo-EM structure of full-length MICAL1 in the autoinhibited state Deposited 2024-02-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1067（1067 aa）	Not recorded	ZN ZINC ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris, pH 7.5, 100 mM NaCl, 2 mM MgCl2, 2 mM DTT. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9EWY CryoEM structure of human MICAL1 Deposited 2024-04-05	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1067（1067 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9G0C Structure of human Mical1 bMERB_V978A_V985A domain:Rab10 complex. Deposited 2024-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 918–1067（150 aa）	Mutation：V978A, V985A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.17 M Sodium acetate, 0.085 M Tris-HCl pH 8.5, 25.5% (w/v) PEG 4000 and 15% (v/v) glycerol	Resolution 1.80 Å R-free 0.231
9G0D Structure of human Mical1 bMERB_V978A domain:Rab10 complex. Deposited 2024-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 918–1067（150 aa）	Mutation：V978A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Imidazole pH 8.0, 5% (w/v) PEG 3000 and 30% (v/v) PEG 200	Resolution 2.05 Å R-free 0.249

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MICA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–118； UniProt 506–614

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	2dk9
Deposition date deposition_date	2006-04-07
Structure title title	Solution structure of Calponin Homology domain of Human MICAL-1
Keywords keywords	helix, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.02 Å
Radius of gyration Rg (electron density) rg_electron	15.41 Å
Forward intensity I(0) i0	908044000.00
Molecular weight molecular_weight	251180.0 kDa
Excluded volume excluded_volume	312300 Å³
Envelope volume envelope_volume	46976 Å³
Hydration-shell volume shell_volume	18813 Å³
Envelope diameter envelope_diameter	71.0 Å
Shell Rg shell_rg	28.25 Å
Envelope Rg envelope_rg	24.52 Å
Shape Rg shape_rg	15.40 Å
Total Rg total_rg	15.75 Å
Total atoms total_atoms	34940
Residues n_residues	2360
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	64.3 Å
Rg (real space) rg_real	16.27 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	9.0800e+08
I(0) uncertainty (real space) i0_real_error	1.1860e+07
Rg (reciprocal space) rg_reciprocal	16.24 Å
I(0) (reciprocal space) i0_reciprocal	908000000.0000
Solution quality estimate total_estimate	0.6877
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.862
Kurtosis Kurtosis kurtosis	0.799
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	643600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.162; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.463; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dk9a1
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.0 — automated matches

Domain ID domain_id	d2dk9a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2dk9A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	10 — Calponin-like domain

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8. Citations (1)

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Description description	NEDD9-interacting protein with calponin homology and LIM domains
Molecular weight formula_weight	12579.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	34940

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/dk/2dk9/2dk9.fit
pddf	/app/data/pr_computation/dk/2dk9/2dk9.pr.out
profile	/app/data/saxs_computation/dk/2dk9/2dk9.dat

Solution structure of Calponin Homology domain of Human MICAL-1

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

NEDD9-interacting protein with calponin homology and LIM domains

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)