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Yorodumi- PDB-8ot2: Structural and functional studies of geldanamycin amide synthase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ot2 | ||||||
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Title | Structural and functional studies of geldanamycin amide synthase ShGdmF | ||||||
Components | GdmF | ||||||
Keywords | BIOSYNTHETIC PROTEIN / amide synthase / geldanamycin / amidase / alpha-beta | ||||||
Function / homology | Arylamine N-acetyltransferase / N-acetyltransferase / arylamine N-acetyltransferase activity / Papain-like cysteine peptidase superfamily / ACETATE ION / DI(HYDROXYETHYL)ETHER / : / GdmF Function and homology information | ||||||
Biological species | Streptomyces hygroscopicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Ewert, W. / Zeilinger, C. / Kirschning, A. / Preller, M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structural and functional studies of geldanamycin amide synthase ShGdmF Authors: Ewert, W. / Bartens, C. / Heutling, A. / Ongouta, J. / Vogt, M. / Kishore, A. / Zeilinger, C. / Preller, M. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ot2.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ot2.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ot2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ot2_validation.pdf.gz | 762.2 KB | Display | wwPDB validaton report |
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Full document | 8ot2_full_validation.pdf.gz | 763.7 KB | Display | |
Data in XML | 8ot2_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 8ot2_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/8ot2 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/8ot2 | HTTPS FTP |
-Related structure data
Related structure data | 8btmC 8oomC 8osvC 8oszC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29838.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: gdmF / Production host: Escherichia coli (E. coli) / References: UniProt: Q84G21 |
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-Non-polymers , 6 types, 85 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-W0E / | Mass: 123.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO / Feature type: SUBJECT OF INVESTIGATION #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.56 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 25 % PEG4000, 150 mM Sodium acetate, 200 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→42.12 Å / Num. obs: 29337 / % possible obs: 97.94 % / Redundancy: 13.1 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0769 / Net I/σ(I): 21.26 |
Reflection shell | Resolution: 1.77→1.833 Å / Rmerge(I) obs: 1.358 / Num. unique obs: 2867 / CC1/2: 0.694 / % possible all: 96.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→42.12 Å / SU ML: 0.1872 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7179 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→42.12 Å
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Refine LS restraints |
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LS refinement shell |
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