[English] 日本語
![](img/lk-miru.gif)
- PDB-1g3p: CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAINS OF BACTERIOPHAGE MINO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1g3p | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAINS OF BACTERIOPHAGE MINOR COAT PROTEIN G3P | ||||||
![]() | MINOR COAT PROTEIN | ||||||
![]() | VIRAL PROTEIN / MINOR COAT PROTEIN / FILAMENTOUS BACTERIOPHAGE / PHAGE DISPLAY / SELECTIVELY INFECTIVE PHAGES | ||||||
Function / homology | ![]() viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / host cell membrane / viral capsid / entry receptor-mediated virion attachment to host cell / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lubkowski, J. / Hennecke, F. / Pluckthun, A. / Wlodawer, A. | ||||||
![]() | ![]() Title: The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p. Authors: Lubkowski, J. / Hennecke, F. / Pluckthun, A. / Wlodawer, A. #1: ![]() Title: Selectively Infective Phage (Sip) Technology: A Novel Method for in Vivo Selection of Interacting Protein-Ligand Pairs Authors: Spada, S. / Pluckthun, A. #2: ![]() Title: The C-Terminal Domain of Tola is the Coreceptor for Filamentous Phage Infection of E. Coli Authors: Riechmann, L. / Holliger, P. #3: ![]() Title: A Conserved Infection Pathway for Filamentous Bacteriophages is Suggested by the Structure of the Membrane Penetration Domain of the Minor Coat Protein G3P from Phage Fd Authors: Holliger, P. / Riechmann, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 57.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 23626.484 Da / Num. of mol.: 1 / Fragment: TWO N-TERMINAL DOMAINS, N1 AND N2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell line (production host): BL21 (DE3), FOR SELENOMETHIONINE-VARIANT DL41 (DE3) Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | MINOR COAT PROTEIN FROM GENE 3 OF FILAMENTOUS BACTERIOPHAGE M13. THE PHAGE COAT PROTEIN (G3P) ...MINOR COAT PROTEIN FROM GENE 3 OF FILAMENTOU |
Nonpolymer details | TRO 21 IS THE OXIDIZED TRP. TRO CARRIES MOST LIKELY AN OXINDOLE SIDE CHAIN (1,3-DIHYDRO-INDOLE-2- ...TRO 21 IS THE OXIDIZED TRP. TRO CARRIES MOST LIKELY AN OXINDOLE SIDE CHAIN (1,3-DIHYDRO-INDOLE-2-ONE). THE OXYGEN ATOM IS BOUND (LIKELY VIA A DOUBLE BOND) TO THE CD1 CARBON. ADDITIONAL |
Sequence details | THE SEQUENCE DIFFERENCES ARE NATURALLY OCCURRING VARIATIONS WHICH DO NOT AFFECT THE FUNCTIONALITY ...THE SEQUENCE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) BUFFERED WITH 50 MM PIPES PH 6.5 AND THE PRECIPITANT (30% PEG 4000, 0.2 M AMMONIUM SULFATE, 2 MM DTT) WERE MIXED AND EQUILIBRATED (IN THE ...Details: EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) BUFFERED WITH 50 MM PIPES PH 6.5 AND THE PRECIPITANT (30% PEG 4000, 0.2 M AMMONIUM SULFATE, 2 MM DTT) WERE MIXED AND EQUILIBRATED (IN THE HANGING DROP SETUP) AGAINST THE PRECIPITANT., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→22 Å / Num. obs: 37511 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.53 % / Rsym value: 0.034 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.11 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 282603 / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.11 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS (USING MAD X-RAY DATA) / Resolution: 1.46→8 Å / Rfactor Rfree error: 0.0037 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: SEVEN RESIDUES WERE REFINED IN TWO ALTERNATE CONFORMATIONS EACH.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.46→1.53 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|