+Open data
-Basic information
Entry | Database: PDB / ID: 4hah | ||||||
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Title | Structure of the Salmonella plasmid virulence C protein (SpvC) | ||||||
Components | 27.5 kDa virulence protein | ||||||
Keywords | LYASE / Phosphothreonine Lyase | ||||||
Function / homology | Function and homology information Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / extracellular region Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shenoy, A.G. / Johnson, S.J. / Hengge, A.C. | ||||||
Citation | Journal: To be Published Title: Mechanistic and structural investigations of phosphothreonine lyase class of enzymes. Authors: Vyacheslav, I.K. / Shenoy, A.G. / Johnson, S.J. / Hengge, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hah.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hah.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hah_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 4hah_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 4hah_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 4hah_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/4hah ftp://data.pdbj.org/pub/pdb/validation_reports/ha/4hah | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27681.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: mkaD, PSLT038, SPV, spvC, vsdD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (RIL) / References: UniProt: P0A2M9 #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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 3350 (a 50% w/v solution) 0.1M Ammonium Chloride (1M stock solution) , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2011 / Details: mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.264 Å / Num. all: 331429 / Num. obs: 45887 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.22 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4573 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.264 Å / SU ML: 0.59 / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.385 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→32.264 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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