+Open data
-Basic information
Entry | Database: PDB / ID: 1t3z | ||||||
---|---|---|---|---|---|---|---|
Title | Formyl-CoA Tranferase mutant Asp169 to Ser | ||||||
Components | Formyl-coenzyme A transferase | ||||||
Keywords | TRANSFERASE / CoA transferase / oxalate / oxalate degradation / intertwined / knotted fold / CAIB-BAIF family / CoA complex | ||||||
Function / homology | Function and homology information formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Oxalobacter formigenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Ricagno, S. / Jonsson, S. / Richards, N.G. / Lindqvist, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes Authors: Jonsson, S. / Ricagno, S. / Lindqvist, Y. / Richards, N.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t3z.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t3z.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 1t3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t3z_validation.pdf.gz | 967.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1t3z_full_validation.pdf.gz | 985.9 KB | Display | |
Data in XML | 1t3z_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 1t3z_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/1t3z ftp://data.pdbj.org/pub/pdb/validation_reports/t3/1t3z | HTTPS FTP |
-Related structure data
Related structure data | 1t4cC 1vgqC 1vgrC 1p5rS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47203.656 Da / Num. of mol.: 2 / Mutation: D169S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oxalobacter formigenes (bacteria) / Gene: FRC / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06644, formyl-CoA transferase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE AUTHOR SAID THAT THE AMINO ACID IN THIS POSITION IS ILE, THE SWS IS INCORRECT. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 56.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Hepes, Mg chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.087 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30.29 Å / Num. all: 50343 / Num. obs: 50343 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 40.3 Å2 / Rsym value: 0.061 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 7322 / Rsym value: 0.337 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1P5R Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.827 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.254 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.397 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|