+Open data
-Basic information
Entry | Database: PDB / ID: 4iix | ||||||
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Title | Structure of MccF in complex with glutamyl sulfamoyl guanosine | ||||||
Components | MccF | ||||||
Keywords | HYDROLASE / carboxypeptidase / ESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.229 Å | ||||||
Authors | Agarwal, V. / Nair, S.K. | ||||||
Citation | Journal: To be Published Title: Structure of MccF with substrate analogs Authors: Agarwal, V. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iix.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iix.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 4iix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iix_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4iix_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4iix_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 4iix_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/4iix ftp://data.pdbj.org/pub/pdb/validation_reports/ii/4iix | HTTPS FTP |
-Related structure data
Related structure data | 4iiyC 3tlaS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 41716.586 Da / Num. of mol.: 2 / Mutation: S118A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccF / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: Q2KKH9, UniProt: Q47511*PLUS, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | #3: Chemical | ChemComp-EDO / #4: 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 Å3/Da / Density % sol: 38.54 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M Tris, pH 7.5, 8% PEG8000, VAPOR DIFFUSION, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2012 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.229→71.583 Å / Num. all: 190319 / Num. obs: 190093 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.075 / Rsym value: 0.09 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.23→1.25 Å / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.415 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TLA Resolution: 1.229→32.837 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.26 / σ(F): 1.38 / Phase error: 15.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.878 Å2 / ksol: 0.383 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.92 Å2 / Biso mean: 10.8321 Å2 / Biso min: 3.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.229→32.837 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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