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Yorodumi- PDB-2qjv: Crystal structure of an iolb-like protein (stm4420) from salmonel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qjv | ||||||
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Title | Crystal structure of an iolb-like protein (stm4420) from salmonella typhimurium lt2 at 1.90 A resolution | ||||||
Components | Uncharacterized IolB-like protein | ||||||
Keywords | ISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella typhimurium LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of uncharacterized IolB-like protein (16422983) from Salmonella typhimurium LT2 at 1.90 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. RESIDUES GLU 161 AND ASP 163 WERE MUTATED TO ALA IN THE EXPRESSED CONSTRUCT. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qjv.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qjv.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qjv_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 2qjv_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 2qjv_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2qjv_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qjv ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qjv | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ALA / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 2 - 264 / Label seq-ID: 3 - 265
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30876.041 Da / Num. of mol.: 2 / Mutation: E161A, D163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Species: Salmonella typhimurium / Strain: LT2, SGSC1412 / Gene: 16422983, STM4420 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ZK62 |
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-Non-polymers , 5 types, 738 molecules
#2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: 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 grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: NANODROP, 0.01M Nickel (II) chloride, 1.0M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97913, 0.97883 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2007 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→29.514 Å / Num. obs: 104039 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.76 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→29.514 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.495 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. FOUR NI IONS, SEVEN CHLORIDE IONS, FOUR SULFATE IONS AND TWO GLYCEROL MOLECULES WERE MODELED. THE PRESENCE OF THE NI ATOMS ARE SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. 5. RESIDUES 1 AND 265 TO 269 IN EACH SUBUNIT ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 6. THE DISUFIDE BOND BETWEEN CYS 212 FROM EACH SUBUNIT IS PARTIALLY REDUCED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.283 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.514 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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