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1ay9

WILD-TYPE UMUD' FROM E. COLI

Method: X-RAY DIFFRACTION Dmax: 92.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

UMUD PROTEIN

OrganismNot specified

UniProt P04153

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 32–139 Chain B； UniProt 32–139 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；100MM CACODYLATE BUFFER PH 6.0 Resolution 3.00 Å R-free 0.287
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 32–139 Chain B； UniProt 32–139 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；100MM CACODYLATE BUFFER PH 6.0 Resolution 3.00 Å R-free 0.287

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 1AY9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1I4V SOLUTION STRUCTURE OF THE UMUD' HOMODIMER Deposited 2001-02-23 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 25–139（115 aa）
Chain B 25–139（115 aa）
Mutation：G25A Mutation：G25A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure ambient
NMR sample composition 0.9 mM UmuD' U-15N; 150 mM NaCl, 10 mM phosphate, pH 6.0, 1mM DTT, 0.1 mM EDTA | 95% H2O/5% D2O
NMR sample composition 1.3 mM UmuD' U-15N,13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 95% H2O/5% D2O
NMR sample composition 1.5 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 95% H20, 5% D2O
NMR sample composition 1.4 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 100% D2O
NMR sample composition 0.5 mM UmuD' U-10% 13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 100% D2O
NMR sample composition 2.7 mM UmuD' U-100% 2H,15N and 2.7 mM unlabeled UmuD'; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA | 95% H20, 5% D2O
Resolution not provided
1UMU STRUCTURE DETERMINATION OF UMUD' BY MAD PHASING OF THE SELENOMETHIONYL PROTEIN Deposited 1996-03-07 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 25–139（115 aa） Fragment：;UMUD', RESIDUES 25 - 139 ;
Chain B 25–139（115 aa） Fragment：;UMUD', RESIDUES 25 - 139 ;
Mutation：DEL(1-24), M138T, M61 AND M110 SUBSTITUTED BY SELENOMETHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：DEL(1-24), M138T, M61 AND M110 SUBSTITUTED BY SELENOMETHIONINE Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.8；THE CRYSTALS WERE GROWN FROM 600MM LISO4, 20MM MGCL2, 100MM CACODYLATE BUFFER PH 5.8, 5MM DTT AT 20C WITH A PROTEIN CONCENTRATION OF 12-15 MG/ML. THE CRYSTALS WERE FROZEN AT 100K IN PARATONE FOR DATA COLLECTION AT THE NSLS X4A BEAMLINE.
Resolution 2.50 Å R-free 0.303

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UMUD_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–108； UniProt 32–139 Author chain B； PDBConstruct 1–108； UniProt 32–139

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 1ay9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ay9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ay9
Deposition date deposition_date1997-11-15
Structure title titleWILD-TYPE UMUD' FROM E. COLI
Keywords keywordsMUTAGENESIS PROTEIN, DNA REPAIR, HYDROLASE; MUTAGENESIS PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.63 Å
Radius of gyration Rg (electron density) rg_electron19.86 Å
Forward intensity I(0) i08819480.00
Molecular weight molecular_weight22630.0 kDa
Excluded volume excluded_volume28708 ų
Envelope volume envelope_volume36744 ų
Hydration-shell volume shell_volume16528 ų
Envelope diameter envelope_diameter94.9 Å
Shell Rg shell_rg24.70 Å
Envelope Rg envelope_rg20.72 Å
Shape Rg shape_rg19.86 Å
Total Rg total_rg20.69 Å
Total atoms total_atoms1592
Residues n_residues216
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 dmax92.2 Å
Rg (real space) rg_real20.68 Å
Rg uncertainty (real space) rg_real_error1.27 Å
I(0) (real space) i0_real8.8190e+06
I(0) uncertainty (real space) i0_real_error1.3380e+05
Rg (reciprocal space) rg_reciprocal20.67 Å
I(0) (reciprocal space) i0_reciprocal8819000.0000
Solution quality estimate total_estimate0.7004
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.0 Å
Skewness Skewness skewness0.537
Kurtosis Kurtosis kurtosis0.589
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1188000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.216; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.453; Smooth: 0.999
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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_idd1ay9a_
Class classb — All beta proteins
Fold Fold foldb.87 — LexA/Signal peptidase
Superfamily Superfamily superfamilyb.87.1 — LexA/Signal peptidase
Family Family familyb.87.1.1 — LexA-related
Domain ID domain_idd1ay9b_
Class classb — All beta proteins
Fold Fold foldb.87 — LexA/Signal peptidase
Superfamily Superfamily superfamilyb.87.1 — LexA/Signal peptidase
Family Family familyb.87.1.1 — LexA-related

CATH v4.4 (2 domains)

Domain ID domain_id1ay9A00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily10 — Umud Fragment, subunit A
Domain ID domain_id1ay9B00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily10 — Umud Fragment, subunit A
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8. Citations (2)

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9. Files and Curves (10)