SAXSdb — 1pp5

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

microcin J25

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 38–58	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：298 K；Ionic strength (raw mmCIF value) NA；Pressure ambient NMR sample composition：2mM Microcin J25 U-13C,15N; 99.5% CD3OH, 0.5% H2O \| 99.5% CD3OH, 0.5% H2O	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 1PP5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Q71 The structure of microcin J25 is a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone Deposited 2003-08-14	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–58（21 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.3 mg of microcin J25 \| 100% CD3OH	Resolution not provided
1S7P Solution structure of thermolysin digested microcin J25 Deposited 2004-01-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 38–47（10 aa） Fragment：Residues 38-47 Chain B 48–58（11 aa） Fragment：Residues 48-58	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 295 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 6mM t-MccJ25 \| 100% CD3OH	Resolution not provided
2MMT Lasso peptide-based integrin inhibitor: Microcin J25 variant with RGDF substitution of Gly12-Ile13-Gly14-Thr15 Deposited 2014-03-18	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–58（21 aa） Fragment：UNP residues 38-58	Mutation：G12R/I13G/G14D/T15F	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure 1.0 NMR sample composition 12.6 mM MCCJ25(RGDF), methanol \| methanol	Resolution not provided
2MMW LASSO PEPTIDE BASED INTEGRIN INHIBITOR: MICROCIN J25 VARIANT WITH RGD SUBSTITUTION of GLY12-ILE13-GLY14 Deposited 2014-03-20	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–58（21 aa）	Mutation：G12R, I13G, G14D	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure ambient NMR sample composition 11.6 mM MCCJ25(RGD), methanol \| methanol	Resolution not provided
4CU4 FhuA from E. coli in complex with the lasso peptide microcin J25 (MccJ25) Deposited 2014-03-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 38–58（21 aa）	Not recorded	FTT 3-HYDROXY-TETRADECANOIC ACID × 4 DAO LAURIC ACID × 1 MYR MYRISTIC ACID × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 20 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE × 1 DPO DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；20 MM TRIS PH 7.5, 120 MM LITHIUM SULFATE, 100 MM SODIUM CITRATE PH 5, 20 % PEG300	Resolution 2.30 Å R-free 0.255
5T56 [3]catenane from MccJ25 G12R/I13C/G21C lasso peptide Deposited 2016-08-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 38–48（11 aa） Chain B 51–57（7 aa） Chain C 38–48（11 aa） Chain D 51–57（7 aa）	Mutation：UNP residues 38-48 Mutation：UNP residues 51-57 Mutation：UNP residues 38-48 Mutation：UNP residues 51-57	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 295 K；Pressure ambient NMR sample composition 3.7 mg/mL [3]catenane from MccJ25 RCC lasso peptide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6N60 Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Microcin J25 (MccJ25) Deposited 2018-11-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain M 38–58（21 aa） Fragment：UNP residues 38-58	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M HEPES, pH 6.7, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol	Resolution 3.68 Å R-free 0.306

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MCJA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–21； UniProt 38–58

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	1pp5
Deposition date deposition_date	2003-06-16
Structure title title	Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot
Keywords keywords	;LARIAT, PROTOKNOT, BACKBONE-SIDECHAIN AMIDE LINKAGE, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, ANTIBIOTIC ;; ANTIBIOTIC
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	6.99 Å
Radius of gyration Rg (electron density) rg_electron	7.48 Å
Forward intensity I(0) i0	5538390.00
Molecular weight molecular_weight	20914.0 kDa
Excluded volume excluded_volume	26741 Å³
Envelope volume envelope_volume	3741 Å³
Hydration-shell volume shell_volume	4436 Å³
Envelope diameter envelope_diameter	28.9 Å
Shell Rg shell_rg	12.52 Å
Envelope Rg envelope_rg	8.53 Å
Shape Rg shape_rg	7.45 Å
Total Rg total_rg	8.03 Å
Total atoms total_atoms	2880
Residues n_residues	210
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	24.3 Å
Rg (real space) rg_real	7.10 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	5.5380e+06
I(0) uncertainty (real space) i0_real_error	5.9180e+04
Rg (reciprocal space) rg_reciprocal	7.10 Å
I(0) (reciprocal space) i0_reciprocal	5538000.0000
Solution quality estimate total_estimate	0.8082
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	7.4 Å
Skewness Skewness skewness	0.568
Kurtosis Kurtosis kurtosis	-0.217
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1016.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 0.960; Sysdev: 1.000; Positv: 1.000; Valcen: 0.615; Smooth: 0.957

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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

SCOP 2.08 (1 domains)

Domain ID domain_id	d1pp5a_
Class class	j — Peptides
Fold Fold fold	j.5 — Macrocyclic bacteriocins
Superfamily Superfamily superfamily	j.5.1 — Macrocyclic bacteriocins
Family Family family	j.5.1.1 — Microcin J25

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8. Citations (1)

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Description description	microcin J25
Molecular weight formula_weight	2126.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2880

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

fit	/app/data/saxs_computation/pp/1pp5/1pp5.fit
pddf	/app/data/pr_computation/pp/1pp5/1pp5.pr.out
profile	/app/data/saxs_computation/pp/1pp5/1pp5.dat

Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot

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

microcin J25

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)