+Open data
-Basic information
Entry | Database: PDB / ID: 5ac3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PAM12A | ||||||
Components | PEPTIDE AMIDASE | ||||||
Keywords | HYDROLASE / MUTAGENESIS | ||||||
Function / homology | Function and homology information Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | STENOTROPHOMONAS MALTOPHILIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wu, B. / Wijma, H.J. / Song, L. / Rozeboom, H.J. / Poloni, C. / Tian, Y. / Arif, M.I. / Nuijens, T. / Quadflieg, P.J.L.M. / Szymanski, W. ...Wu, B. / Wijma, H.J. / Song, L. / Rozeboom, H.J. / Poloni, C. / Tian, Y. / Arif, M.I. / Nuijens, T. / Quadflieg, P.J.L.M. / Szymanski, W. / Feringa, B.L. / Janssen, D.B. | ||||||
Citation | Journal: Acs Catalysis / Year: 2016 Title: Versatile Peptide C-Terminal Functionalization Via a Computationally Peptide Amidase Authors: Wu, B. / Wijma, H.J. / Song, L. / Rozeboom, H.J. / Poloni, C. / Tian, Y. / Arif, M.I. / Nuijens, T. / Quadflieg, P.J.L.M. / Szymanski, W. / Feringa, B.L. / Janssen, D.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ac3.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ac3.ent.gz | 159.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ac3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ac3_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ac3_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 5ac3_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 5ac3_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/5ac3 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5ac3 | HTTPS FTP |
-Related structure data
Related structure data | 1m22S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 54990.926 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STENOTROPHOMONAS MALTOPHILIA (bacteria) Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): TOP10 / References: UniProt: Q8RJN5, amidase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-ACY / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: VAPOR DIFFUSION, HANGING DROP, 1.0 M SODIUM ACETATE, 0.1 M HEPES PH 7.0, 0.02M CADMIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2014 / Details: HELIOSMX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.4 Å / Num. obs: 42172 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M22 Resolution: 1.8→71.77 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.394 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→71.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|