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Yorodumi- PDB-8b05: TRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b05 | ||||||
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Title | TRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plunger after 20 sec | ||||||
Components | (Tryptophan synthase ...) x 2 | ||||||
Keywords | LYASE / Trytophan Synthase / Time-resolved crystallography | ||||||
Function / homology | Function and homology information tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography. Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b05.cif.gz | 310.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b05.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 8b05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b05_validation.pdf.gz | 821.7 KB | Display | wwPDB validaton report |
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Full document | 8b05_full_validation.pdf.gz | 827.8 KB | Display | |
Data in XML | 8b05_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 8b05_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/8b05 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/8b05 | HTTPS FTP |
-Related structure data
Related structure data | 8aw8C 8aw9C 8awbC 8awcC 8awdC 8aweC 8awfC 8awsC 8awuC 8awvC 8awxC 8awyC 8b03C 8b06C 8b08C 8b2oC 8b2vC 8b2wC 8b3mC 2wsyS S: Starting model for refinement 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
-Tryptophan synthase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28698.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42918.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: trpB, STM1726 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 5 types, 245 molecules
#3: Chemical | ChemComp-CS / | ||
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#4: Chemical | ChemComp-PLS / [ | ||
#5: Chemical | ChemComp-IND / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-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: 2.55 Å3/Da / Density % sol: 51.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 300, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 7, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→45.1 Å / Num. obs: 40992 / % possible obs: 99.2 % / Redundancy: 7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.11 / Rrim(I) all: 0.292 / Net I/σ(I): 6.4 / Num. measured all: 285529 / Scaling rejects: 194 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WSY Resolution: 2.1→45.1 Å / SU ML: 0.2091 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.126 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: 37.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→45.1 Å
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Refine LS restraints |
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LS refinement shell |
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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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