SAXSdb — 1xmk

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

Double-stranded RNA-specific adenosine deaminase

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 294–366	Not recorded	CD CADMIUM ION × 2 NI NICKEL (II) ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；312 K；PEG1000, Cadmium Chloride, Nickel Chloride, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 312K, pH 9.00	Resolution 0.97 Å R-free 0.183

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 1XMK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QBJ CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX Deposited 1999-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA Chain B 133–209（77 aa） Fragment：N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；HANGING DROP VAPOR DIFFUSION OVER 1.6 M (NH4)2SO4, 10 % GLYCEROL AT 24 DEGREES CELSIUS, pH 5.6	Resolution 2.10 Å R-free 0.265
1QBJ CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX Deposited 1999-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-TERMINAL HELIX-TURN-HELIX DOMAIN ZALPHA	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；HANGING DROP VAPOR DIFFUSION OVER 1.6 M (NH4)2SO4, 10 % GLYCEROL AT 24 DEGREES CELSIUS, pH 5.6	Resolution 2.10 Å R-free 0.265
1QGP NMR STRUCTURE OF THE Z-ALPHA DOMAIN OF ADAR1, 15 STRUCTURES Deposited 1999-05-03	Different construct Different mutation/modification 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 125–201（77 aa） Fragment：Z-ALPHA DOMAIN	Mutation：C125S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 0.137 M NACL；Pressure 1 NMR sample composition NA-PHOSPHATE	Resolution not provided
2ACJ Crystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins Deposited 2005-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Fragment：Zalpha domain, ADAR1 Chain B 140–202（63 aa） Fragment：Zalpha domain, ADAR1 Chain C 140–202（63 aa） Fragment：Zalpha domain, ADAR1 Chain D 140–202（63 aa） Fragment：Zalpha domain, ADAR1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；22-23% MPD, 55-60mM sodium acetate, 15-16mM calsium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.60 Å R-free 0.285
2GXB Crystal Structure of The Za Domain bound to Z-RNA Deposited 2006-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 140–202（63 aa） Fragment：Za Domain Chain B 140–202（63 aa） Fragment：Za Domain	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；292 K；40% PEG600, 100mM Sodium Acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.25 Å R-free 0.244
2L54 Solution structure of the Zalpha domain mutant of ADAR1 (N43A,Y47A) Deposited 2010-10-24	Different construct Different mutation/modification 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 136–198（63 aa） Fragment：DRADA 1 domain, UNP residues 136-198	Mutation：N43A, Y47A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR sample composition 50 mM sodium phosphate-1, 50 mM sodium chloride-2, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MDR Solution structure of the third double-stranded RNA-binding domain (dsRBD3) of human adenosine-deaminase ADAR1 Deposited 2013-09-17	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 708–801（94 aa） Fragment：UNP residues 708-801	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 0.7-0.9 mM [U-99% 13C; U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-0.9 mM [U-99% 13C; U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition 0.7-0.9 mM [U-99% 15N] dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-0.9 mM dsRBD3, 20 mM sodium phosphate, 100 mM potassium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3F21 Crystal structure of Zalpha in complex with d(CACGTG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209 Chain B 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.279
3F21 Crystal structure of Zalpha in complex with d(CACGTG) Deposited 2008-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.279
3F22 Crystal structure of Zalpha in complex with d(CGTACG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209 Chain B 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.269
3F22 Crystal structure of Zalpha in complex with d(CGTACG) Deposited 2008-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.269
3F23 Crystal structure of Zalpha in complex with d(CGGCCG) Deposited 2008-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209 Chain B 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.264
3F23 Crystal structure of Zalpha in complex with d(CGGCCG) Deposited 2008-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 133–209（77 aa） Fragment：N-terminal zalpha Domain, UNP residues 133-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；2.2M (NH4)2SO4, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.264
3IRQ Crystal structure of a Z-Z junction Deposited 2009-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Fragment：Zalpha domain Chain B 140–202（63 aa） Fragment：Zalpha domain Chain C 140–202（63 aa） Fragment：Zalpha domain Chain D 140–202（63 aa） Fragment：Zalpha domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；17% PEG 2000, 0.1 M Tris-HCl, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.271
3IRR Crystal Structure of a Z-Z junction (with HEPES intercalating) Deposited 2009-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Fragment：Zalpha domain Chain B 140–202（63 aa） Fragment：Zalpha domain Chain C 140–202（63 aa） Fragment：Zalpha domain Chain D 140–202（63 aa） Fragment：Zalpha domain	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；16% PEG 2000 MME, 0.1 M HEPES, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.65 Å R-free 0.283
5ZU1 Crystal Structure of BZ junction in diverse sequence Deposited 2018-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–198（59 aa） Chain B 140–198（59 aa） Chain C 140–198（59 aa） Chain D 140–198（59 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 4.5；296 K；25% 2-methyl-2,4-pentanediol (MPD), 100mM NaOAC, pH 4.5	Resolution 3.01 Å R-free 0.280
5ZUO Crystal Structure of BZ junction in diverse sequence Deposited 2018-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Chain B 140–202（63 aa） Chain C 140–202（63 aa） Chain D 140–202（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；296 K；20% dioxane, with microseeding of small crystals	Resolution 2.90 Å R-free 0.301
5ZUP Crystal Structure of BZ junction in diverse sequence Deposited 2018-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 140–202（63 aa） Chain B 140–202（63 aa） Chain C 140–202（63 aa） Chain D 140–202（63 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；296 K；25% ethylene glycol, with microseeding of small crystal	Resolution 2.90 Å R-free 0.282
7C0I Crystal structure of chimeric mutant of E3L in complex with Z-DNA Deposited 2020-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 169–184（16 aa） Chain A 192–193（2 aa） Chain A 195–195（1 aa） Chain B 169–184（16 aa） Chain B 192–193（2 aa） Chain B 195–195（1 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；Sodium citrate pH 4.0, Ammonium sulfate, ethylene glycol	Resolution 2.40 Å R-free 0.227
7C0I Crystal structure of chimeric mutant of E3L in complex with Z-DNA Deposited 2020-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 169–184（16 aa） Chain C 192–193（2 aa） Chain C 195–195（1 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；Sodium citrate pH 4.0, Ammonium sulfate, ethylene glycol	Resolution 2.40 Å R-free 0.227
7C0J Crystal structure of chimeric mutant of GH5 in complex with Z-DNA Deposited 2020-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 169–178（10 aa） Chain A 192–192（1 aa） Chain A 195–195（1 aa） Chain B 169–178（10 aa） Chain B 192–192（1 aa） Chain B 195–195（1 aa）	Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES pH 6.0, PEG 4000, ethylene glycol	Resolution 2.75 Å R-free 0.248
7ZJ1 Crystal structure of ADAR1-dsRBD3 dimer Deposited 2022-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 716–797（82 aa） Chain B 716–797（82 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；100 mM sodium citrate pH 4.0, 20% (w/v) PEG 6000, and 1.0 M LiCl	Resolution 1.65 Å R-free 0.225
7ZLQ Crystal structure of ADAR1-dsRBD3 dimer in complex with dsRNA Deposited 2022-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 716–797（82 aa） Chain B 716–797（82 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM sodium cacodylate, 5% (w/v) PEG 4000, 30 mM CaCl2, 230 mM KCl	Resolution 2.80 Å R-free 0.266
8GBC Homo sapiens Zalpha mutant - N173S Deposited 2023-02-25	Different construct Different mutation/modification 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 140–202（63 aa）	Mutation：N173S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；277 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 2 mM [U-13C; U-15N] protein, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
8GBD Homo sapiens Zalpha mutant - P193A Deposited 2023-02-25	Different construct Different mutation/modification 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 140–202（63 aa）	Mutation：P193A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；277 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 2 mM [U-13C; U-15N] protein, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
9B83 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from human GLI1 gene Deposited 2024-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 127–1226（1100 aa） Chain B 127–1226（1100 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9B84 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene Deposited 2024-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 127–1226（1100 aa） Chain B 127–1226（1100 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9B89 Cryo-EM structure of human ADAR1 in complex with dsRNA derived from HT2C gene in the pre-editing state Deposited 2024-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 127–1226（1100 aa） Chain B 127–1226（1100 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 2 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å

23 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DSRAD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–79； UniProt 294–366

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	1xmk
Deposition date deposition_date	2004-10-03
Structure title title	The Crystal structure of the Zb domain from the RNA editing enzyme ADAR1
Keywords keywords	winged Helix-Turn-Helix, RNA editing, Interferon, ADAR1, 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	13.16 Å
Radius of gyration Rg (electron density) rg_electron	12.14 Å
Forward intensity I(0) i0	2134200.00
Molecular weight molecular_weight	9330.0 kDa
Excluded volume excluded_volume	11338 Å³
Envelope volume envelope_volume	12817 Å³
Hydration-shell volume shell_volume	9246 Å³
Envelope diameter envelope_diameter	44.0 Å
Shell Rg shell_rg	17.60 Å
Envelope Rg envelope_rg	12.68 Å
Shape Rg shape_rg	12.17 Å
Total Rg total_rg	13.34 Å
Total atoms total_atoms	632
Residues n_residues	79
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	45.8 Å
Rg (real space) rg_real	13.09 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.1340e+06
I(0) uncertainty (real space) i0_real_error	2.2900e+04
Rg (reciprocal space) rg_reciprocal	13.09 Å
I(0) (reciprocal space) i0_reciprocal	2134000.0000
Solution quality estimate total_estimate	0.8511
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.8 Å
Skewness Skewness skewness	0.186
Kurtosis Kurtosis kurtosis	-0.158
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	245400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Double-stranded RNA-specific adenosine deaminase
Molecular weight formula_weight	9005.4 kDa
EC 编号 ec_number	3.5.4.-
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	793

GSHMASLDMAEIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTTPPIWHLTDKKRERMQIK

来源 Source

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)

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xmka1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.19 — Z-DNA binding domain

Domain ID domain_id	d1xmka2
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	1xmkA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (3)

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Unit-cell length a length_a	35.557 Å
Unit-cell length b length_b	43.526 Å
Unit-cell length c length_c	45.471 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	4

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

Resolution resolution	0.970 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1450
R_work r_work	—
R_free r_free	0.1830

fit	/app/data/saxs_computation/xm/1xmk/1xmk.fit
pddf	/app/data/pr_computation/xm/1xmk/1xmk.pr.out
profile	/app/data/saxs_computation/xm/1xmk/1xmk.dat

The Crystal structure of the Zb domain from the RNA editing enzyme ADAR1

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

Double-stranded RNA-specific adenosine deaminase

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