+Open data
-Basic information
Entry | Database: PDB / ID: 1iu4 | ||||||
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Title | Crystal Structure Analysis of the Microbial Transglutaminase | ||||||
Components | microbial transglutaminase | ||||||
Keywords | TRANSFERASE / ALPHA-BETA | ||||||
Function / homology | Function and homology information protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity Similarity search - Function | ||||||
Biological species | Streptomyces mobaraensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å | ||||||
Authors | Kashiwagi, T. / Yokoyama, K. / Ishikawa, K. / Ono, K. / Ejima, D. / Matsui, H. / Suzuki, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of microbial transglutaminase from Streptoverticillium mobaraense Authors: Kashiwagi, T. / Yokoyama, K. / Ishikawa, K. / Ono, K. / Ejima, D. / Matsui, H. / Suzuki, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iu4.cif.gz | 281.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iu4.ent.gz | 228.1 KB | Display | PDB format |
PDBx/mmJSON format | 1iu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iu4_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 1iu4_full_validation.pdf.gz | 511.3 KB | Display | |
Data in XML | 1iu4_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 1iu4_validation.cif.gz | 82.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/1iu4 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/1iu4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The protein acts as a monomer. |
-Components
#1: Protein | Mass: 37918.414 Da / Num. of mol.: 4 / Fragment: residues 1-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P81453, protein-glutamine gamma-glutamyltransferase #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: 2.39 Å3/Da / Density % sol: 48.57 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG1000, calcium chloride, cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||
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: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Dec 2, 1999 |
Radiation | Monochromator: Si(111) (Joham type) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 187008 / Num. obs: 55351 / % possible obs: 0.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.38 % / Biso Wilson estimate: 26.25 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.13 / % possible all: 0.921 |
Reflection | *PLUS % possible obs: 0.98 % / Num. measured all: 187008 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 92.1 % / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→40 Å / σ(F): 2 Stereochemistry target values: standard set of QUANTA release98 (MSI)
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.199 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |