2y7c

Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

Method: ELECTRON MICROSCOPY Dmax: 127.5 Å Quality: GOOD

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

TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN

OrganismNot specified

UniProt P05719

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–464 Not recorded TYPE I RESTRICTION ENZYME ECOKI M PROTEIN × 2 (P08957) GENE 0.3 PROTEIN × 2 (P03775) ELECTRON MICROSCOPY cryo-EM buffer:20MM TRIS-CL, 100 MM NACL;pH 4.7;20MM TRIS-CL, 100 MM NACL Resolution 18.00 Å

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T1SK_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–464; UniProt 1–464

TYPE I RESTRICTION ENZYME ECOKI M PROTEIN

OrganismNot specified

UniProt P08957

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–529 Chain C; UniProt 1–529 Not recorded TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN × 1 (P05719) GENE 0.3 PROTEIN × 2 (P03775) ELECTRON MICROSCOPY cryo-EM buffer:20MM TRIS-CL, 100 MM NACL;pH 4.7;20MM TRIS-CL, 100 MM NACL Resolution 18.00 Å

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T1MK_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–529; UniProt 1–529 Author chain C; PDBConstruct 1–529; UniProt 1–529

GENE 0.3 PROTEIN

ENTEROBACTERIA PHAGE T7

UniProt P03775

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–116 Chain E; UniProt 1–116 Not recorded TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN × 1 (P05719) TYPE I RESTRICTION ENZYME ECOKI M PROTEIN × 2 (P08957) ELECTRON MICROSCOPY cryo-EM buffer:20MM TRIS-CL, 100 MM NACL;pH 4.7;20MM TRIS-CL, 100 MM NACL Resolution 18.00 Å

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.

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name V03_BPT7
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–116; UniProt 1–116 Author chain E; PDBConstruct 1–116; UniProt 1–116

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 2y7c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2y7c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2y7c
Deposition date deposition_date2011-01-31
Structure title titleAtomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.
Keywords keywordsTRANSFERASE; TRANSFERASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier40.48
Radius of gyration Rg (electron density) rg_electron39.76
Forward intensity I(0) i0590653000.00
Molecular weight molecular_weight194870.0 kDa
Excluded volume excluded_volume242540 ų
Envelope volume envelope_volume356150 ų
Hydration-shell volume shell_volume72504 ų
Envelope diameter envelope_diameter135.4
Shell Rg shell_rg47.13
Envelope Rg envelope_rg39.05
Shape Rg shape_rg39.75
Total Rg total_rg40.20
Total atoms total_atoms13725
Residues n_residues1735
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.5
Rg (real space) rg_real40.29
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real5.9070e+08
I(0) uncertainty (real space) i0_real_error1.1010e+07
Rg (reciprocal space) rg_reciprocal40.47
I(0) (reciprocal space) i0_reciprocal590800000.0000
Solution quality estimate total_estimate0.8850
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.3
Skewness Skewness skewness0.144
Kurtosis Kurtosis kurtosis-0.370
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha71330000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.853

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)