[English] 日本語
![](img/lk-miru.gif)
- PDB-2wkb: Crystal Structure of Macrophage Migration Inhibitory Factor from ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2wkb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Macrophage Migration Inhibitory Factor from Plasmodium berghei | ||||||
![]() | MACROPHAGE MIGRATION INHIBITORY FACTOR | ||||||
![]() | CYTOKINE | ||||||
Function / homology | Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / 2-Layer Sandwich / Alpha Beta / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dobson, S.E. / Augustijn, K.D. / Brannigan, J.A. / Dodson, E.J. / Waters, A.P. / Wilkinson, A.J. | ||||||
![]() | ![]() Title: The Crystal Structures of Macrophage Migration Inhibition Factor (Mif) from Plasmodium Falciparum and Plasmodium Berghei. Authors: Dobson, S.E. / Augustijn, K.D. / Brannigan, J.A. / Schnick, C. / Janse, C.J. / Dodson, E.J. / Waters, A.P. / Wilkinson, A.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 155.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 124.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 535.9 KB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wkfC ![]() 2os5S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9979, -0.0204, 0.0621), Vector: |
-
Components
#1: Protein | Mass: 14109.884 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-116 Source method: isolated from a genetically manipulated source Details: CYS2 IS MODIFIED TO CME IN ALL CHAINS DUE TO BINDING TO BETA-MERCAPTOETHANOL Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Nonpolymer details | S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CME): BETA MERCAPTOETHANOL IS COVALENTLY BOUND TO CYS2 VIA A ...S,S-(2-HYDROXYETH | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.06 % / Description: NONE |
---|---|
Crystal grow | pH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 13% PEG 6000, 0.2 M KSCN |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 72962 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.35 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.36 / % possible all: 95.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2OS5 Resolution: 1.78→70.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.872 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.256 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→70.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|