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1zgw

NMR structure of E. Coli Ada protein in complex with DNA

Method: SOLUTION NMR Dmax: 66.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ada polyprotein

Escherichia coli

UniProt P06134

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 1–139 Fragment：N-terminal domain Non-standard monomer：Yes (specific site not provided by mmCIF) 5'-D(*GP*CP*AP*AP*AP*TP*TP*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*A)-3' × 1 5'-D(*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*TP*AP*AP*TP*TP*TP*GP*C)-3' × 1 ZN ZINC ION × 1 SOLUTION NMR NMR measurement conditions：pH 6.5；303 K；Ionic strength (raw mmCIF value) 25 mM sodium phosphate; 50 mM NaCl; 5 mM DTT；Pressure ambient NMR sample composition：13C; 15N; 70% 2H | 90% H2O/10% D2O NMR sample composition：15N | 90% H20, 10% D2O NMR sample composition：15N; Ile delta1, Leu delta1, delta2, Val gamma1, gamma2 13C; 2H | D2O NMR sample composition：Val, Ile, Leu Methyl group 13C; Phe and Tyr 1H; 2H | 90% H2O/10% D2O NMR sample composition：15N, 2H | 90% H2O/10% D2O NMR sample composition：10% 13C | D2O NMR sample composition：13C C5A labeled thymine top or bottom strand; unlabeled protein | D2O NMR sample composition：13C; 15N; 2H | 90% H2O, 10% D20 NMR sample composition：13C | D2O NMR sample composition：15N | 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 1ZGW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ADN SOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN OF ESCHERICHIA COLI ADA Deposited 1993-09-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–92（92 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1EYF REFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN OF E. COLI ADA Deposited 2000-05-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–92（92 aa） Fragment：N-TERMINAL 10 KDA DOMAIN
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.4；298 K；Pressure ambient
NMR measurement conditions pH 6.4；298 K；Pressure ambient
NMR measurement conditions pH 6.4；298 K；Pressure ambient
NMR measurement conditions pH 6.4；298 K；Pressure ambient
NMR sample composition 2 mM N-Ada10; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 2 mM N-Ada10; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 100% D2O | 90% H2O/10% D2O
NMR sample composition 2 mM N-Ada10 U-15N; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O | 100% D2O
NMR sample composition 2 mM N-Ada10 U-15N, 13C; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1SFE ADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM ESCHERICHIA COLI Deposited 1996-06-21 Different construct Different mutation/modification Different oligomeric state 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 175–354（180 aa） Fragment：C-TERMINAL 19KD OF THE ADA PROTEIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1U8B Crystal structure of the methylated N-ADA/DNA complex Deposited 2004-08-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain A 9–139（131 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；100 mM sodium cacodylate, 100 mM NaCl, 50 mM magnesium chloride, 20% OEG 8000, pH 6.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.274
1WPK Methylated Form of N-terminal Transcriptional Regulator Domain of Escherichia Coli Ada Protein Deposited 2004-09-07 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–146（146 aa） Fragment：Methylated N-terminal 16 kDa Domain
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 300mM NaCl；Pressure ambient
NMR sample composition 1mM Protein U-15N,13C; 50mM phosphate buffer with 5mM 2-mercaptoethanol NA; 85% H2O, 15% D2O | 85% H2O, 15% D2O
NMR sample composition 1mM Protein U-15N,13C; 50mM phosphate buffer with 5mM 2-mercaptoethanol ; 99.9% D2O | 99.9% D2O
Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADA_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–139； UniProt 1–139

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 1zgw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zgw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zgw
Deposition date deposition_date2005-04-22
Structure title titleNMR structure of E. Coli Ada protein in complex with DNA
Keywords keywordsProtein-DNA complex, helix-turn-helix, Zinc ligand, TRANSCRIPTION REGULATOR-DNA COMPLEX; TRANSCRIPTION REGULATOR/DNA
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.57 Å
Radius of gyration Rg (electron density) rg_electron20.51 Å
Forward intensity I(0) i06845380000.00
Molecular weight molecular_weight539690.0 kDa
Excluded volume excluded_volume607260 ų
Envelope volume envelope_volume55955 ų
Hydration-shell volume shell_volume21719 ų
Envelope diameter envelope_diameter75.2 Å
Shell Rg shell_rg28.25 Å
Envelope Rg envelope_rg22.22 Å
Shape Rg shape_rg20.49 Å
Total Rg total_rg20.62 Å
Total atoms total_atoms67280
Residues n_residues3480
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 dmax66.4 Å
Rg (real space) rg_real20.64 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real6.8450e+09
I(0) uncertainty (real space) i0_real_error1.0320e+08
Rg (reciprocal space) rg_reciprocal20.63 Å
I(0) (reciprocal space) i0_reciprocal6845000000.0000
Solution quality estimate total_estimate0.6979
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary20.2 Å
Skewness Skewness skewness0.389
Kurtosis Kurtosis kurtosis-0.419
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1837000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.925; Smooth: 0.652
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id1zgwA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology10 — DNA Methylphosphotriester Repair Domain
Homologous superfamily homologous superfamily10 — DNA Methylphosphotriester Repair Domain
Domain ID domain_id1zgwA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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8. Citations (1)

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9. Files and Curves (10)