+Open data
-Basic information
Entry | Database: PDB / ID: 3q98 | ||||||
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Title | Structure of ygeW encoded protein from E. coli | ||||||
Components | transcarbamylase | ||||||
Keywords | TRANSFERASE / Rossmann Fold / Unknown transcarbamylase | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / carboxyl- or carbamoyltransferase activity / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / amino acid metabolic process / amino acid binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å | ||||||
Authors | Li, Y. / Jing, Z. / Yu, X. / Allewell, N.M. / Tuchman, M. / Shi, D. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: The ygeW encoded protein from Escherichia coli is a knotted ancestral catabolic transcarbamylase. Authors: Li, Y. / Jin, Z. / Yu, X. / Allewell, N.M. / Tuchman, M. / Shi, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q98.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q98.ent.gz | 133.6 KB | Display | PDB format |
PDBx/mmJSON format | 3q98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q98_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 3q98_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 3q98_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3q98_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/3q98 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/3q98 | 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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Unit cell |
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-Components
#1: Protein | Mass: 45228.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygeW / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1R7G1, UniProt: Q46803*PLUS |
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#2: 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: 1.96 Å3/Da / Density % sol: 37.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3350, 200 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97933 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 23528 / Num. obs: 23411 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1686 / % possible all: 96.1 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.001→28.067 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8505 / SU ML: 0.23 / σ(F): 0.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.562 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 232.16 Å2 / Biso mean: 35.5349 Å2 / Biso min: 12.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→28.067 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 23.0719 Å / Origin y: 49.4722 Å / Origin z: 46.1146 Å
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Refinement TLS group |
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