[English] 日本語
Yorodumi- PDB-1mkf: VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mkf | ||||||
---|---|---|---|---|---|---|---|
Title | VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68 | ||||||
Components | M3 | ||||||
Keywords | IMMUNE SYSTEM / HERPESVIRUS / VIRAL IMMUNE EVASION / CHEMOKINE BINDING PROTEIN / DECOY RECEPTOR / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Murid herpesvirus 4 (Murine herpesvirus 68) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å | ||||||
Authors | Alexander, J.M. / Fremont, D.H. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor Authors: Alexander, J.M. / Nelson, C.A. / Van Berkel, V. / Lau, E.K. / Studts, J.M. / Brett, T.J. / Speck, S.H. / Handel, T.M. / Virgin, H.W. / Fremont, D.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1mkf.cif.gz | 154.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1mkf.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mkf_validation.pdf.gz | 372.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1mkf_full_validation.pdf.gz | 386.5 KB | Display | |
Data in XML | 1mkf_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1mkf_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mkf ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mkf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41826.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68) Genus: Rhadinovirus / Gene: M3 / Plasmid: pFB-1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O41925 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 18% PEG4000, 100MM CACL2, 100MM IMIDAZOLE/MALIC ACID PH 5.1, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.1 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 43484 / Num. obs: 43484 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 40.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.346 / % possible all: 97 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Redundancy: 3.1 % / Num. measured all: 133215 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 97 % / Rmerge(I) obs: 0.346 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 25464.2 / Data cutoff high rms absF: 25464.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 57.7995 Å2 / ksol: 0.341932 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 2506 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å |