[English] 日本語
![](img/lk-miru.gif)
- PDB-3go0: Crystal structure of D-enantiomer of human alpha-defensin 1 (D-HNP1) -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3go0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of D-enantiomer of human alpha-defensin 1 (D-HNP1) | ||||||
![]() | Neutrophil defensin 1 | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | polypeptide(D) / polypeptide(D) (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pazgier, M. / Lu, W.-Y. | ||||||
![]() | ![]() Title: Through the looking glass, mechanistic insights from enantiomeric human defensins. Authors: Wei, G. / de Leeuw, E. / Pazgier, M. / Yuan, W. / Zou, G. / Wang, J. / Ericksen, B. / Lu, W.Y. / Lehrer, R.I. / Lu, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 26.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 20.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3gnySC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DAL / Beg label comp-ID: DAL / End auth comp-ID: DCY / End label comp-ID: DCY / Refine code: 6 / Auth seq-ID: 1 - 30 / Label seq-ID: 1 - 30
|
-
Components
#1: Polypeptide(D) | Mass: 3452.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D-enantiomer / Source: (synth.) ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Sequence details | THE SEQUENCE DATABASE REFERENCE FOR THE L-FORM SEQUENCE IS UNP ENTRY P59665 AND INCLUDES RESIDUES ...THE SEQUENCE DATABASE REFERENCE FOR THE L-FORM SEQUENCE IS UNP ENTRY P59665 AND INCLUDES RESIDUES 65-94. THE SEQUENCE TRANSLATES | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.11 % |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 sodium citrate tribasic dehydrate, 0.1 M HEPES, pH 7.5, 20% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2008 / Details: confocal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.56→40.281 Å / Num. all: 8495 / Num. obs: 8404 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.078 / Rsym value: 0.112 |
Reflection shell | Resolution: 1.56→1.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 9.7 / Num. unique all: 339 / Rsym value: 0.204 / % possible all: 84.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3GNY Resolution: 1.56→12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.191 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.091 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES, RESIDUAL ONLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.72 Å2 / Biso mean: 16.886 Å2 / Biso min: 9.62 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→12 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 238 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.56→1.603 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|