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Yorodumi- PDB-3exz: Crystal structure of the MaoC-like dehydratase from Rhodospirillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3exz | ||||||
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Title | Crystal structure of the MaoC-like dehydratase from Rhodospirillum rubrum. Northeast Structural Genomics Consortium target RrR103a. | ||||||
Components | MaoC-like dehydratase | ||||||
Keywords | LYASE / MaoC-like dehydratase / Q2RSA1_RHORT / NESG / RrR103a / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / MaoC-like dehydratase Function and homology information | ||||||
Biological species | Rhodospirillum rubrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the MaoC-like dehydratase from Rhodospirillum rubrum. Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3exz.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3exz.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 3exz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3exz_validation.pdf.gz | 468.8 KB | Display | wwPDB validaton report |
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Full document | 3exz_full_validation.pdf.gz | 485.7 KB | Display | |
Data in XML | 3exz_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 3exz_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/3exz ftp://data.pdbj.org/pub/pdb/validation_reports/ex/3exz | 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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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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Details | authors state that the biological assembly is Dimer according to aggregation screening. Chain A form a dimer with symmetry mate though symmetry operation -x+1, y, -z-1. |
-Components
#1: Protein | Mass: 16954.799 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Strain: ATCC 11170 / Gene: Rru_A2194 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q2RSA1 #2: 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: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.75M K(2)HPO(4), 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 76686 / Num. obs: 75459 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 5.9 / Num. unique all: 7619 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→38.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 149295.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.2593 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→38.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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