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Yorodumi- PDB-3eqx: CRYSTAL STRUCTURE OF A FIC FAMILY PROTEIN (SO_4266) FROM SHEWANEL... -
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-Basic information
Entry | Database: PDB / ID: 3eqx | |||||||||
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Title | CRYSTAL STRUCTURE OF A FIC FAMILY PROTEIN (SO_4266) FROM SHEWANELLA ONEIDENSIS AT 1.6 A RESOLUTION | |||||||||
Components | FIC DOMAIN CONTAINING TRANSCRIPTIONAL REGULATOR | |||||||||
Keywords | DNA BINDING PROTEIN / FIC FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | |||||||||
Function / homology | Function and homology information AMPylase activity / protein adenylyltransferase / protein adenylylation / magnesium ion binding / protein homodimerization activity / ATP binding Similarity search - Function | |||||||||
Biological species | Shewanella oneidensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution. Authors: Das, D. / Krishna, S.S. / McMullan, D. / Miller, M.D. / Xu, Q. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M.C. ...Authors: Das, D. / Krishna, S.S. / McMullan, D. / Miller, M.D. / Xu, Q. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elias, Y. / Elsliger, M.A. / Ernst, D. / Feuerhelm, J. / Grzechnik, A. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H. / Trame, C.B. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Hodgson, K.O. / Wooley, J. / 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 | 3eqx.cif.gz | 177.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eqx.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 3eqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eqx_validation.pdf.gz | 447.3 KB | Display | wwPDB validaton report |
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Full document | 3eqx_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 3eqx_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3eqx_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/3eqx ftp://data.pdbj.org/pub/pdb/validation_reports/eq/3eqx | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Refine code: 6 / Auth seq-ID: 11 - 370 / Label seq-ID: 11 - 370
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Details | AUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 42650.926 Da / Num. of mol.: 2 / Mutation: G109C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: NP_719793.1, SO_4266 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8E9K5 #2: Chemical | ChemComp-PGE / | #3: 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: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.2M NaF, 20.0% PEG-3350, No Buffer pH 7.1, 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: 0.91837,0.97905,0.97935 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2007 / 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: 1.6→29.553 Å / Num. obs: 106471 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.465 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.83 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.6→29.553 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.098 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.083 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. MODELING EXPERIMENTS SUGGEST THAT THE ELECTRON DENSITY NEAR THE HPFXXGNG MOTIF (PRESENT IN FIC PROTEINS) STARTING AT HIS198 IN CHAIN A IS LIKELY TO BE A PORTION (B1-B4) OF THE PARTIALLY MISSING N-TERMINUS OF CHAIN B FROM A SYMMETRY RELATED MOLECULE. B1(MSE) IS SUPPORTED BY A SIGNIGICANT PEAK IN THE ANOMALOUS DIFFERENCE FOURIER MAP CALCULATED FOR THIS SELENOMETHIONINE DERIVATIZED PROTEIN CRYSTAL. 5. PGE HAS BEEN MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. RESIDUES A344-A345 IN CHAIN A AND B5-B10 ARE DISORDERED AND HAVE NOT BEEN MODELLED.
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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 max: 68.52 Å2 / Biso mean: 23.39 Å2 / Biso min: 10.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.553 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 / Number: 4510 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.6→1.641 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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