+Open data
-Basic information
Entry | Database: PDB / ID: 4mxm | ||||||
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Title | Crystal structure of superantigen pfit | ||||||
Components | Transcriptional regulator I2 | ||||||
Keywords | DNA BINDING PROTEIN / Superantigen | ||||||
Function / homology | Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Liu, L.H. / Chen, H. / Li, H.M. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: Pfit is a structurally novel Crohn's disease-associated superantigen. Authors: Liu, L. / Chen, H. / Brecher, M.B. / Li, Z. / Wei, B. / Nandi, B. / Zhang, J. / Ling, H. / Winslow, G. / Braun, J. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mxm.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mxm.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mxm_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 4mxm_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 4mxm_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 4mxm_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/4mxm ftp://data.pdbj.org/pub/pdb/validation_reports/mx/4mxm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22953.010 Da / Num. of mol.: 2 / Fragment: transcriptional regulator I2: unp residues 10-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: A506 / Gene: I2, pfiT, PflA506_3695 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I2BPL4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 4-8% PEG 3350, 0.1 M Tris, 0.2 M ammonium acetate, 5 mM MgCl2, 5 mM DTT, 5% isopropanol, and 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2005 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.7 Å / Num. all: 35150 / Num. obs: 35150 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.694 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→29.212 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 28.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.594 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→29.212 Å
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Refine LS restraints |
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LS refinement shell |
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