← Back to search
5prn

E1M, Y96W, S119W MUTANT OF RH. BLASTICA PORIN

Method: X-RAY DIFFRACTION Dmax: 68.0 Å Quality: GOOD
▼

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

PORIN

Rhodobacter blasticus

UniProt P39767

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 2–289 Mutation：E1M, Y96W, S119W C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 9 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.8；pH 7.8 Resolution 2.00 Å R-free 0.188

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 5PRN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BH3 E1M, A116K MUTANT OF RH. BLASTICA PORIN Deposited 1998-06-12 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–289（288 aa）
Mutation：E1M, A116K C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；DROP: PROTEIN 5MG/ML, TRISCL 20MM PH=7.2, LICL 300MM, NAN3 3 MM, PEG600 10-18% RESERVOIR: PEG600 30-38%
Resolution 2.19 Å R-free 0.181
1H6S Asymmetric conductivity of engineered proteins Deposited 2001-06-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 1–203（203 aa）
Chain 1 204–289（86 aa）
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；50 MM NAOAC PH 4.75, 100 MM (NH4)2SO4, 5.5 % PEG4000
Resolution 3.00 Å R-free 0.210
1PRN REFINED STRUCTURE OF PORIN FROM RHODOPSEUDOMONAS BLASTICA AND COMPARISON WITH THE PORIN FROM RHODOBACTER CAPSULATUS Deposited 1994-07-13 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–289（289 aa）
Not recorded C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 9 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.96 Å
2PRN RHODOPSEUDOMONAS BLASTICA PORIN, TRIPLE MUTANT E1M, E99W, A116W Deposited 1998-06-12 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–289（288 aa）
Mutation：E1M, E99W, A116W MG MAGNESIUM ION × 3 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 1.93 Å R-free 0.205
3PRN E1M, A104W MUTANT OF RH. BLASTICA PORIN Deposited 1998-06-12 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–289（288 aa）
Mutation：E1M, A104W MG MAGNESIUM ION × 3 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 1.90 Å R-free 0.190
6PRN E1M, K50A, R52A MUTANT OF RH. BLASTICA PORIN Deposited 1998-06-12 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–289（288 aa）
Mutation：E1M, K50A, R52A C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 2.04 Å R-free 0.186
7PRN E1M, D97A, E99A MUTANT OF RH. BLASTICA PORIN Deposited 1998-06-12 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–289（288 aa）
Mutation：E1M, D97A, E99A C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 2.25 Å R-free 0.222
8PRN E1M, K50A, R52A, D97A, E99A MUTANT OF RH. BLASTICA PORIN Deposited 1998-06-12 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–289（288 aa）
Mutation：E1M, K50A, R52A, D97A, E99A C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.30 Å R-free 0.215

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PORI_RHOBL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–289； UniProt 2–289

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 5prn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5prn
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5prn
Deposition date deposition_date1998-06-12
Structure title titleE1M, Y96W, S119W MUTANT OF RH. BLASTICA PORIN
Keywords keywordsINTEGRAL MEMBRANE PROTEIN, PORIN, PORE EYELET MUTANT, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier20.72 Å
Radius of gyration Rg (electron density) rg_electron20.12 Å
Forward intensity I(0) i017676100.00
Molecular weight molecular_weight31614.0 kDa
Excluded volume excluded_volume39307 ų
Envelope volume envelope_volume49895 ų
Hydration-shell volume shell_volume20446 ų
Envelope diameter envelope_diameter69.3 Å
Shell Rg shell_rg27.14 Å
Envelope Rg envelope_rg20.04 Å
Shape Rg shape_rg20.08 Å
Total Rg total_rg21.18 Å
Total atoms total_atoms2236
Residues n_residues289
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
▼

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

Maximum dimension Dmax dmax68.0 Å
Rg (real space) rg_real20.58 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real1.7680e+07
I(0) uncertainty (real space) i0_real_error1.9930e+05
Rg (reciprocal space) rg_reciprocal20.60 Å
I(0) (reciprocal space) i0_reciprocal17680000.0000
Solution quality estimate total_estimate0.8683
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5 Å
Skewness Skewness skewness0.077
Kurtosis Kurtosis kurtosis-0.321
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2258000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.973
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5prna_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamilyf.4.3 — Porins
Family Family familyf.4.3.1 — Porin

CATH v4.4 (1 domains)

Domain ID domain_id5prnA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology160 — Porin
Homologous superfamily homologous superfamily10 — Porin
▶

8. Citations (3)

▶

9. Files and Curves (10)