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2mdr

Solution structure of the third double-stranded RNA-binding domain (dsRBD3) of human adenosine-deaminase ADAR1

Method: SOLUTION NMR Dmax: 55.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Double-stranded RNA-specific adenosine deaminase

Homo sapiens

UniProt P55265

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 708–801 Fragment：UNP residues 708-801 No other associated polymer 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

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 2MDR 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 experimental method 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 experimental method 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 experimental conditions 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
1XMK The Crystal structure of the Zb domain from the RNA editing enzyme ADAR1 Deposited 2004-10-03 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 294–366（73 aa）
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
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 experimental method 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 method 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 experimental conditions 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
3F21 Crystal structure of Zalpha in complex with d(CACGTG) Deposited 2008-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 method 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 experimental method 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 experimental method 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 experimental method 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 method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental conditions 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 experimental conditions 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 20–113； UniProt 708–801

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2mdr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2mdr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2mdr
Deposition date deposition_date2013-09-17
Structure title titleSolution structure of the third double-stranded RNA-binding domain (dsRBD3) of human adenosine-deaminase ADAR1
Keywords keywordsdeaminase, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.83 Å
Radius of gyration Rg (electron density) rg_electron14.62 Å
Forward intensity I(0) i0605927000.00
Molecular weight molecular_weight208780.0 kDa
Excluded volume excluded_volume261860 ų
Envelope volume envelope_volume29772 ų
Hydration-shell volume shell_volume14460 ų
Envelope diameter envelope_diameter63.0 Å
Shell Rg shell_rg23.56 Å
Envelope Rg envelope_rg18.95 Å
Shape Rg shape_rg14.56 Å
Total Rg total_rg15.04 Å
Total atoms total_atoms29580
Residues n_residues1880
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax55.1 Å
Rg (real space) rg_real14.96 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real6.0590e+08
I(0) uncertainty (real space) i0_real_error7.2800e+06
Rg (reciprocal space) rg_reciprocal14.95 Å
I(0) (reciprocal space) i0_reciprocal605900000.0000
Solution quality estimate total_estimate0.7228
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary16.1 Å
Skewness Skewness skewness0.578
Kurtosis Kurtosis kurtosis0.148
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha184900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.582; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.650; Smooth: 0.000
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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2mdrA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)