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Yorodumi- PDB-4xgp: Crystal Structure of E112A/H234A Mutant of Stationary Phase Survi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xgp | ||||||
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Title | Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium co-crystallized and soaked with AMP. | ||||||
Components | 5'/3'-nucleotidase SurE | ||||||
Keywords | HYDROLASE / Stationary phase survival protein / Domain swapping / Rossmann fold like / Phosphatase | ||||||
Function / homology | Function and homology information 3'-nucleotidase / 3'-nucleotidase activity / exopolyphosphatase / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mathiharan, Y.K. / Murthy, M.R.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein. Authors: Mathiharan, Y.K. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xgp.cif.gz | 230.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xgp.ent.gz | 183 KB | Display | PDB format |
PDBx/mmJSON format | 4xgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/4xgp ftp://data.pdbj.org/pub/pdb/validation_reports/xg/4xgp | HTTPS FTP |
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-Related structure data
Related structure data | 4rytC 4ryuC 4xepC 4xerSC 4xgbC 4xh8C 4xj7C 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28490.008 Da / Num. of mol.: 4 / Mutation: E112A, H234A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Strain: LT2 / Gene: surE, STM2927 / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase, exopolyphosphatase |
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-Non-polymers , 5 types, 1002 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ADE / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.43 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 4.6 Details: 0.02 M calcium chloride, 0.1 M sodium acetate (pH 4.6) and 30 % 2-Methyl 2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2014 |
Radiation | Monochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→32.87 Å / Num. obs: 111344 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.94 Å2 / Rsym value: 0.07 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 1.9 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XER Resolution: 1.9→32.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.93 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.887 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→32.87 Å
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Refine LS restraints |
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