+Open data
-Basic information
Entry | Database: PDB / ID: 1gmx | ||||||
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Title | Escherichia coli GlpE sulfurtransferase | ||||||
Components | THIOSULFATE SULFURTRANSFERASE GLPE | ||||||
Keywords | TRANSFERASE / RHODANESE / SULFURTRANSFERASE / GLYCEROL METABOLISM | ||||||
Function / homology | Function and homology information sulfur utilization / thiosulfate sulfurtransferase / glycerol metabolic process / thiosulfate sulfurtransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.1 Å | ||||||
Authors | Spallarossa, A. / Donahue, J.T. / Larson, T.J. / Bolognesi, M. / Bordo, D. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Escherichia Coli Glpe is a Prototype Sulfurtransferase for the Single-Domain Rhodanese Homology Superfamily Authors: Spallarossa, A. / Donahue, J.T. / Larson, T.J. / Bolognesi, M. / Bordo, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gmx.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gmx.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gmx_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 1gmx_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 1gmx_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1gmx_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/1gmx ftp://data.pdbj.org/pub/pdb/validation_reports/gm/1gmx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12124.485 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6V5, thiosulfate sulfurtransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 |
Detector | Date: Oct 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→20 Å / Num. obs: 45040 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 1.2 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 43 |
Reflection shell | Resolution: 1.06→1.08 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3 / % possible all: 93.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 555366 |
Reflection shell | *PLUS % possible obs: 93.6 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.1→47 Å / SU B: 0.75 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R Free: 0.03
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Refinement step | Cycle: LAST / Resolution: 1.1→47 Å
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Refinement | *PLUS Highest resolution: 1.06 Å / Lowest resolution: 47 Å / % reflection Rfree: 5 % / Rfactor obs: 0.128 / Rfactor Rfree: 0.151 / Rfactor Rwork: 0.128 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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