[English] 日本語
Yorodumi- PDB-3k6w: Apo and ligand bound structures of ModA from the archaeon Methano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k6w | ||||||
---|---|---|---|---|---|---|---|
Title | Apo and ligand bound structures of ModA from the archaeon Methanosarcina acetivorans | ||||||
Components | Solute-binding protein MA_0280 | ||||||
Keywords | TRANSPORT PROTEIN / ModA / molybdate / Methanosarcina acetivorans / periplasmic binding protein / ABC transporter / ligand / metal-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanosarcina acetivorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å | ||||||
Authors | Chan, S. / Chernishof, I. / Giuroiu, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans Authors: Chan, S. / Giuroiu, I. / Chernishof, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3k6w.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3k6w.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k6w_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3k6w_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 3k6w_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3k6w_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/3k6w ftp://data.pdbj.org/pub/pdb/validation_reports/k6/3k6w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39160.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal TEV-cleavable 6xHis-tag / Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0280, MA_0280 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q8TTZ5 | ||
---|---|---|---|
#2: Chemical | ChemComp-MOO / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow |
|
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.45→54.07 Å / Num. obs: 13167 / % possible obs: 93.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.071 / Χ2: 1.002 / Net I/σ(I): 13.9 | |||||||||||||||
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2 / Num. unique all: 1265 / Rsym value: 0.431 / Χ2: 0.992 / % possible all: 91.4 |
-Phasing
Phasing | Method: molecular replacement | ||||||
---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 0.386 / Cor.coef. Fo:Fc: 0.646
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→54.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.832 / SU B: 17.964 / SU ML: 0.202 / SU R Cruickshank DPI: 0.516 / SU Rfree: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.516 / ESU R Free: 0.259 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.09 Å2 / Biso mean: 37.046 Å2 / Biso min: 9.05 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→54.07 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 18.3706 Å / Origin y: 21.4695 Å / Origin z: -7.0296 Å
|