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1myl

SUBSTITUTING HYDROPHOBIC RESIDUES FOR A BURIED SALT BRIDGE ENHANCES PROTEIN STABILITY BUT DOES NOT REDUCE CONFORMATIONAL SPECIFICITY

Method: X-RAY DIFFRACTION Dmax: 87.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ARC REPRESSOR

Enterobacteria phage P22

UniProt P03050

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 1–53 Chain B； UniProt 1–53 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å R-free 0.293
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 1–53 Chain F； UniProt 1–53 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å R-free 0.293
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–53 Chain D； UniProt 1–53 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å R-free 0.293

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 1MYL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ARQ RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR Deposited 1993-08-24 Different experimental method Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–53（53 aa）
Chain B 1–53（53 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1ARR RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR Deposited 1993-08-24 Different experimental method Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–53（53 aa）
Chain B 1–53（53 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1B28 ARC REPRESSOR MYL MUTANT FROM SALMONELLA BACTERIOPHAGE P22 Deposited 1998-12-05 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 1–53（53 aa）
Chain B 1–53（53 aa）
Mutation：CHAIN A: R31M,E36Y,R40L, CHAIN B: R131M,E136Y,R140L Mutation：CHAIN A: R31M,E36Y,R40L, CHAIN B: R131M,E136Y,R140L No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM KPI, 150 mM NACL
Resolution not provided
1BAZ ARC REPRESSOR MUTANT PHE10VAL Deposited 1998-04-21 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 1–53（53 aa）
Chain B 1–53（53 aa）
Chain C 1–53（53 aa）
Chain D 1–53（53 aa）
Mutation：F10V Mutation：F10V Mutation：F10V Mutation：F10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；PROTEIN WAS CRYSTALLIZED FROM 40-45% SATURATED AMMONIUM PHOSPHATE, PH 8.0, BY MACROSEEDING USING CRYSTALS OF THE WILD TYPE PROTEIN
Resolution 1.90 Å R-free 0.273
1BDT WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX Deposited 1998-05-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–53（53 aa）
Chain B 1–53（53 aa）
Chain C 1–53（53 aa）
Chain D 1–53（53 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.50 Å R-free 0.282
1MYK CRYSTAL STRUCTURE, FOLDING, AND OPERATOR BINDING OF THE HYPERSTABLE ARC REPRESSOR MUTANT PL8 Deposited 1994-10-12 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–53（53 aa）
Chain B 1–53（53 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.277
1NLA Solution Structure of Switch Arc, a Mutant with 3(10) Helices Replacing a Wild-Type Beta-Ribbon Deposited 2003-01-06 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 1–53（53 aa）
Chain B 1–53（53 aa）
Mutation：N11L, L12N Mutation：N11L, L12N No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.8；303 K；Ionic strength (raw mmCIF value) 20mM phosphate；Pressure ambient
NMR measurement conditions pH 4.8；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient
NMR measurement conditions pH 4.67；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate, 150 mM KCl；Pressure ambient
NMR sample composition 4 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc) | 90% H2O/10% D2O
NMR sample composition 7.5 mM 10% 13C-labelled Arc repressor NL11/LN12 (Switch Arc) | 90% H2O, 10% D20
NMR sample composition 5 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc) | 100% D2O
Resolution not provided
1PAR DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE Deposited 1994-03-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric
Chain A 1–53（53 aa）
Chain B 1–53（53 aa）
Chain C 1–53（53 aa）
Chain D 1–53（53 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；pH 7.40, VAPOR DIFFUSION, HANGING DROP
Resolution 2.60 Å
1QTG AVERAGED NMR MODEL OF SWITCH ARC, A DOUBLE MUTANT OF ARC REPRESSOR Deposited 1999-06-27 Different mutation/modification Different experimental method Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–53（53 aa）
Chain B 1–53（53 aa）
Mutation：N11L, L12N Mutation：N11L, L12N No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RARC_BPP22
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–53； UniProt 1–53 Author chain B； PDBConstruct 1–53； UniProt 1–53 Author chain C； PDBConstruct 1–53； UniProt 1–53 Author chain D； PDBConstruct 1–53； UniProt 1–53 Author chain E； PDBConstruct 1–53； UniProt 1–53 Author chain F； PDBConstruct 1–53； UniProt 1–53

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 1myl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1myl
Deposition date deposition_date1994-10-06
Structure title titleSUBSTITUTING HYDROPHOBIC RESIDUES FOR A BURIED SALT BRIDGE ENHANCES PROTEIN STABILITY BUT DOES NOT REDUCE CONFORMATIONAL SPECIFICITY
Keywords keywordsTRANSCRIPTION REGULATION, HYPERSTABLE MUTANT; TRANSCRIPTION REGULATION
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_guinier25.27 Å
Radius of gyration Rg (electron density) rg_electron25.08 Å
Forward intensity I(0) i015744700.00
Molecular weight molecular_weight30488.0 kDa
Excluded volume excluded_volume38376 ų
Envelope volume envelope_volume47968 ų
Hydration-shell volume shell_volume18088 ų
Envelope diameter envelope_diameter89.0 Å
Shell Rg shell_rg29.23 Å
Envelope Rg envelope_rg25.23 Å
Shape Rg shape_rg25.05 Å
Total Rg total_rg25.72 Å
Total atoms total_atoms2140
Residues n_residues256
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 dmax87.7 Å
Rg (real space) rg_real25.58 Å
Rg uncertainty (real space) rg_real_error0.84 Å
I(0) (real space) i0_real1.5740e+07
I(0) uncertainty (real space) i0_real_error2.6330e+05
Rg (reciprocal space) rg_reciprocal25.49 Å
I(0) (reciprocal space) i0_reciprocal15740000.0000
Solution quality estimate total_estimate0.7653
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.9 Å
Skewness Skewness skewness0.613
Kurtosis Kurtosis kurtosis-0.288
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8762000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.529; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.417; Smooth: 0.943
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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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1myla_
Class classa — All alpha proteins
Fold Fold folda.43 — Ribbon-helix-helix
Superfamily Superfamily superfamilya.43.1 — Ribbon-helix-helix
Family Family familya.43.1.1 — Arc/Mnt-like phage repressors
Domain ID domain_idd1mylb_
Class classa — All alpha proteins
Fold Fold folda.43 — Ribbon-helix-helix
Superfamily Superfamily superfamilya.43.1 — Ribbon-helix-helix
Family Family familya.43.1.1 — Arc/Mnt-like phage repressors
Domain ID domain_idd1mylc_
Class classa — All alpha proteins
Fold Fold folda.43 — Ribbon-helix-helix
Superfamily Superfamily superfamilya.43.1 — Ribbon-helix-helix
Family Family familya.43.1.1 — Arc/Mnt-like phage repressors
Domain ID domain_idd1myld_
Class classa — All alpha proteins
Fold Fold folda.43 — Ribbon-helix-helix
Superfamily Superfamily superfamilya.43.1 — Ribbon-helix-helix
Family Family familya.43.1.1 — Arc/Mnt-like phage repressors
Domain ID domain_idd1myle_
Class classa — All alpha proteins
Fold Fold folda.43 — Ribbon-helix-helix
Superfamily Superfamily superfamilya.43.1 — Ribbon-helix-helix
Family Family familya.43.1.1 — Arc/Mnt-like phage repressors
Domain ID domain_idd1mylf_
Class classa — All alpha proteins
Fold Fold folda.43 — Ribbon-helix-helix
Superfamily Superfamily superfamilya.43.1 — Ribbon-helix-helix
Family Family familya.43.1.1 — Arc/Mnt-like phage repressors

CATH v4.4 (6 domains)

Domain ID domain_id1mylA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
Domain ID domain_id1mylB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
Domain ID domain_id1mylC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
Domain ID domain_id1mylD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
Domain ID domain_id1mylE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
Domain ID domain_id1mylF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily10 — Met repressor-like
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8. Citations (2)

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9. Files and Curves (10)