SAXSdb — 1umu

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

UMUD'

Escherichia coli

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 25–139 Chain B； UniProt 25–139	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)	No other associated polymer	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

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 1UMU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AY9 WILD-TYPE UMUD' FROM E. COLI Deposited 1997-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 32–139（108 aa） Chain B 32–139（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；100MM CACODYLATE BUFFER PH 6.0	Resolution 3.00 Å R-free 0.287
1AY9 WILD-TYPE UMUD' FROM E. COLI Deposited 1997-11-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 32–139（108 aa） Chain B 32–139（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；100MM CACODYLATE BUFFER PH 6.0	Resolution 3.00 Å R-free 0.287
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

2 other PDB entries and 3 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 1–116； UniProt 25–139 Author chain B； PDBConstruct 1–116； UniProt 25–139

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1umu
Deposition date deposition_date	1996-03-07
Structure title title	STRUCTURE DETERMINATION OF UMUD' BY MAD PHASING OF THE SELENOMETHIONYL PROTEIN
Keywords keywords	INDUCED MUTAGENESIS, SOS MUTAGENESIS, DNA REPAIR, BETA-LACTAMASE CLEAVAGE REACTION, LEXA REPRESSOR, LAMBDA CI; SOS MUTAGENESIS
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	20.16 Å
Radius of gyration Rg (electron density) rg_electron	19.45 Å
Forward intensity I(0) i0	8691070.00
Molecular weight molecular_weight	22315.0 kDa
Excluded volume excluded_volume	28150 Å³
Envelope volume envelope_volume	35018 Å³
Hydration-shell volume shell_volume	16100 Å³
Envelope diameter envelope_diameter	94.2 Å
Shell Rg shell_rg	24.33 Å
Envelope Rg envelope_rg	20.37 Å
Shape Rg shape_rg	19.47 Å
Total Rg total_rg	20.19 Å
Total atoms total_atoms	1559
Residues n_residues	207
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	90.1 Å
Rg (real space) rg_real	20.21 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	8.6910e+06
I(0) uncertainty (real space) i0_real_error	1.3730e+05
Rg (reciprocal space) rg_reciprocal	20.20 Å
I(0) (reciprocal space) i0_reciprocal	8691000.0000
Solution quality estimate total_estimate	0.7072
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.518
Kurtosis Kurtosis kurtosis	0.517
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1054000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.231; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.497; Smooth: 0.998

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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_id	d1umua_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.1 — LexA-related

Domain ID domain_id	d1umub_
Class class	b — All beta proteins
Fold Fold fold	b.87 — LexA/Signal peptidase
Superfamily Superfamily superfamily	b.87.1 — LexA/Signal peptidase
Family Family family	b.87.1.1 — LexA-related

CATH v4.4 (2 domains)

Domain ID domain_id	1umuA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

Domain ID domain_id	1umuB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	109 — Umud Fragment, subunit A
Homologous superfamily homologous superfamily	10 — Umud Fragment, subunit A

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8. Citations (2)

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Unit-cell length a length_a	52.800 Å
Unit-cell length b length_b	52.800 Å
Unit-cell length c length_c	160.100 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.3030

Description description	UMUD'
Molecular weight formula_weight	12429.7 kDa
EC 编号 ec_number	3.4.21.-
Mutation mutation	DEL(1-24), M138T, M61 AND M110 SUBSTITUTED BY SELENOMETHIONINE
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1636

STRUCTURE DETERMINATION OF UMUD' BY MAD PHASING OF THE SELENOMETHIONYL PROTEIN

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

UMUD'

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

fit	/app/data/saxs_computation/um/1umu/1umu.fit
pddf	/app/data/pr_computation/um/1umu/1umu.pr.out
profile	/app/data/saxs_computation/um/1umu/1umu.dat