+Open data
-Basic information
Entry | Database: PDB / ID: 3ngk | ||||||
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Title | PduA from Salmonella enterica Typhimurium | ||||||
Components | Propanediol utilization protein pduA | ||||||
Keywords | UNKNOWN FUNCTION / BMC shell protein / Pdu / Carboxysome / propanediol | ||||||
Function / homology | Function and homology information propanediol degradation polyhedral organelle / propanediol catabolic process Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2608 Å | ||||||
Authors | Crowley, C.S. / Cascio, D. / Sawaya, M.R. / Yeates, T.O. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell. Authors: Crowley, C.S. / Cascio, D. / Sawaya, M.R. / Kopstein, J.S. / Bobik, T.A. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ngk.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ngk.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ngk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/3ngk ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ngk | HTTPS FTP |
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-Related structure data
Related structure data | 3n79C 3i6pS S: Starting model for refinement C: citing same article (ref.) |
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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: 10591.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: pduA, STM2038 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A1C7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 500 mM LiSO4, 20% 1,2 propanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→90 Å / Num. all: 3039 / Num. obs: 3039 / % possible obs: 66.2 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Rmerge(I) obs: 0.271 / Χ2: 1.577 / Net I/σ(I): 3.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3I6P Resolution: 2.2608→33.576 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8037 / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.433 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.64 Å2 / Biso mean: 17.2944 Å2 / Biso min: 6.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2608→33.576 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: 2
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