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Yorodumi- PDB-3dcx: Crystal structure of a duf1696 family protein with a pleckstrin-h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dcx | ||||||
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Title | Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution | ||||||
Components | Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains | ||||||
Keywords | UNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Bacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain superfamily / Bacterial PH domain / PH-domain like / Roll / Mainly Beta / bPH_1 domain-containing protein Function and homology information | ||||||
Biological species | Shewanella loihica PV-4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. Authors: Xu, Q. / Bateman, A. / Finn, R.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / ...Authors: Xu, Q. / Bateman, A. / Finn, R.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Ernst, D. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dcx.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dcx.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dcx_validation.pdf.gz | 473.7 KB | Display | wwPDB validaton report |
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Full document | 3dcx_full_validation.pdf.gz | 479.7 KB | Display | |
Data in XML | 3dcx_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 3dcx_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/3dcx ftp://data.pdbj.org/pub/pdb/validation_reports/dc/3dcx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End label comp-ID: LEU / Refine code: 4
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Details | AUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A PENTAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 13109.577 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella loihica PV-4 (bacteria) / Gene: YP_001092950.1, Shew_0819 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QB43 #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.83 Details: 37.0% 2-methyl-2,4-pentanediol, 0.15M sodium chloride, 0.1M HEPES pH 6.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97925,0.91837,0.97871 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→29.828 Å / Num. obs: 43831 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.05 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.19 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2→29.828 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.891 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.159 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. MPD AND CL ARE PRESENT IN CRYSTALLIZATION CONDITION.
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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: 25.932 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.828 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1157 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 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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