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Yorodumi- PDB-2fno: Crystal structure of a glutathione s-transferase (atu5508) from a... -
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-Basic information
Entry | Database: PDB / ID: 2fno | |||||||||
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Title | Crystal structure of a glutathione s-transferase (atu5508) from agrobacterium tumefaciens str. c58 at 2.00 A resolution | |||||||||
Components | AGR_pAT_752p | |||||||||
Keywords | TRANSFERASE / Thioredoxin fold / gst c-terminal domain-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Agrobacterium tumefaciens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: Proteins / Year: 2006 Title: Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution. Authors: Kosloff, M. / Han, G.W. / Krishna, S.S. / Schwarzenbacher, R. / Fasnacht, M. / Elsliger, M.A. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / ...Authors: Kosloff, M. / Han, G.W. / Krishna, S.S. / Schwarzenbacher, R. / Fasnacht, M. / Elsliger, M.A. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / Chiu, H.J. / Clayton, T. / DiDonato, M. / Duan, L. / Feuerhelm, J. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Johnson, H. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kreusch, A. / Kuhn, P. / Levin, I. / McMullan, D. / Miller, M.D. / Morse, A.T. / Moy, K. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Page, R. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C.L. / Sims, E. / Spraggon, G. / Sridhar, V. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / White, A. / Wolf, G. / Xu, Q. / 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 | 2fno.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fno.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/2fno ftp://data.pdbj.org/pub/pdb/validation_reports/fn/2fno | 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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2 |
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3 |
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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: ASP / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 3 - 236 / Label seq-ID: 15 - 248
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-Components
#1: Protein | Mass: 27898.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: 15162326 / Production host: Escherichia coli (E. coli) / References: GenBank: 15162326, UniProt: Q7D2W7*PLUS #2: Chemical | ChemComp-SCN / #3: 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 | Density Matthews: 2.67 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop Details: 18.00% PEG 3350, 0.2M Potassium Thiocyanate, 10.00% Glycerol, additive - 0.01M spermine tetra-HCL, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979127, 0.964062, 0.979291 | ||||||||||||
Detector | Type: SBC / Detector: CCD / Date: Feb 22, 2004 Details: Water cooled, Sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror | ||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→44.6 Å / Num. obs: 37755 / % possible obs: 95 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.191 / Net I/σ(I): 18.9 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / % possible obs: 64.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 5008 / Χ2: 0.998 / % possible all: 78.1 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→44.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.607 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE ARE LARGE DIFFERENCE FOURIER PEAKS ON THE CRYSTALLOGRAPHIC 2-FOLD AXIS BETWEEN NEAR ASP 107 AND ASP 110 AND SYMMETRY COPIES ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE ARE LARGE DIFFERENCE FOURIER PEAKS ON THE CRYSTALLOGRAPHIC 2-FOLD AXIS BETWEEN NEAR ASP 107 AND ASP 110 AND SYMMETRY COPIES FORMING THE BIOLOGICAL UNIT IN BOTH MONOMERS (A AND B). THESE PEAKS WERE LEFT UNMODELED. 3. THE N-TERMINAL REGION OF MOLECULE B IS LESS WELL ORDERED A PEAK IS OBSERVED IN THE DIFFERENCE MAP FOR THE SE ATOM FROM RESIDUE B1 WHICH WAS NOT MODELED. 4. RESIDUE GLN 73 IS A RAMACHANDRAN OUTLIER IN BOTH CHAINS. THE ELECTRON DENSITY IS GOOD IN THIS REGION AND CLEARLY SUPPORTS THIS BACKBONE CONFORMATION.
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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: 11.467 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.55 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: 2→2.047 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 | Refine-ID: X-RAY DIFFRACTION / Selection: all
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