SAXSdb — 2mmt

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

Microcin J25 RGDF mutant

OrganismNot specified

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	Fragment：UNP residues 38-58 Mutation：G12R/I13G/G14D/T15F	No other associated polymer	SOLUTION NMR NMR measurement conditions：298 K；Pressure 1.0 NMR sample composition：12.6 mM MCCJ25(RGDF), methanol \| methanol	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 2MMT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PP5 Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot Deposited 2003-06-16	Different construct Different mutation/modification 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) 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
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 construct Different mutation/modification 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
2MMW LASSO PEPTIDE BASED INTEGRIN INHIBITOR: MICROCIN J25 VARIANT WITH RGD SUBSTITUTION of GLY12-ILE13-GLY14 Deposited 2014-03-20	Different construct 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 construct Different mutation/modification 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 mutation/modification 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_ECOLX
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	2mmt
Deposition date deposition_date	2014-03-18
Structure title title	Lasso peptide-based integrin inhibitor: Microcin J25 variant with RGDF substitution of Gly12-Ile13-Gly14-Thr15
Keywords keywords	lasso peptide, epitope grafting, integrin inhibitor, drug design, molecular scaffolds, molecular dynamics, 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	8.43 Å
Radius of gyration Rg (electron density) rg_electron	8.42 Å
Forward intensity I(0) i0	15023300.00
Molecular weight molecular_weight	33833.0 kDa
Excluded volume excluded_volume	42683 Å³
Envelope volume envelope_volume	3834 Å³
Hydration-shell volume shell_volume	4285 Å³
Envelope diameter envelope_diameter	33.0 Å
Shell Rg shell_rg	13.14 Å
Envelope Rg envelope_rg	9.69 Å
Shape Rg shape_rg	8.37 Å
Total Rg total_rg	8.83 Å
Total atoms total_atoms	4575
Residues n_residues	315
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	32.6 Å
Rg (real space) rg_real	8.62 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.5020e+07
I(0) uncertainty (real space) i0_real_error	1.5520e+05
Rg (reciprocal space) rg_reciprocal	8.62 Å
I(0) (reciprocal space) i0_reciprocal	15020000.0000
Solution quality estimate total_estimate	0.6921
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	7.8 Å
Skewness Skewness skewness	0.619
Kurtosis Kurtosis kurtosis	-0.282
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1881.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.360; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.079; Smooth: 0.845

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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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8. Citations (1)

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Description description	Microcin J25 RGDF mutant
Molecular weight formula_weight	2274.5 kDa
Mutation mutation	G12R/I13G/G14D/T15F
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4575

fit	/app/data/saxs_computation/mm/2mmt/2mmt.fit
pddf	/app/data/pr_computation/mm/2mmt/2mmt.pr.out
profile	/app/data/saxs_computation/mm/2mmt/2mmt.dat

Lasso peptide-based integrin inhibitor: Microcin J25 variant with RGDF substitution of Gly12-Ile13-Gly14-Thr15

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

Microcin J25 RGDF mutant

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)