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Yorodumi- PDB-4pwu: Crystal structure of a modulator protein MzrA (KPN_03524) from Kl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pwu | ||||||
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Title | Crystal structure of a modulator protein MzrA (KPN_03524) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.45 A resolution | ||||||
Components | Modulator protein MzrA | ||||||
Keywords | SIGNALING PROTEIN / ferredoxin-like fold / PF13721 family (SecD-TM1) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information regulation of protein kinase activity / plasma membrane => GO:0005886 / protein kinase binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a modulator protein MzrA (KPN_03524) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.45 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pwu.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pwu.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/4pwu ftp://data.pdbj.org/pub/pdb/validation_reports/pw/4pwu | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10640.900 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: MGH 78578 / Gene: mzrA, KPN78578_34950, KPN_03524 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6TED5 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (32-128) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (32-128) WAS EXPRESSED WITH A PURIFICATI | |
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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: 1.98 Å3/Da / Density % sol: 37.76 % Description: THE STRUCTURE WAS SOLVED BY THREE-WAVELENGTH MAD DATA COLLECTED AT 2.8A RESOLUTION, AND REFINED AGAINST A HIGHER RESOLUTION DATA (2.45A) COLLECTED FROM THE SAME CRYSTAL. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.83 Details: 1.40M sodium acetate, 0.1M sodium cacodylate pH 5.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2013 Details: Vertical focusing mirror; double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.45→37.573 Å / Num. obs: 12229 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.56 % / Biso Wilson estimate: 66.057 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.84 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 2.45→37.573 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.9091 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. GLYCEROL(GOL) MODELED ARE PRESENT IN CRYO CONDITION.
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Displacement parameters | Biso max: 192.89 Å2 / Biso mean: 81.6489 Å2 / Biso min: 41.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.424 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→37.573 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.68 Å / Total num. of bins used: 6
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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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