+Open data
-Basic information
Entry | Database: PDB / ID: 5hai | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | P99 beta-lactamase mutant - S64G | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / serine beta-lactamase | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | |||||||||
Biological species | Enterobacter cloacae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | |||||||||
Authors | Stojanoski, V. / Adamski, C.J. / Hu, L. / Mehta, S.C. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.G. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain. Authors: Stojanoski, V. / Adamski, C.J. / Hu, L. / Mehta, S.C. / Sankaran, B. / Zwart, P. / Prasad, B.V. / Palzkill, T. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hai.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hai.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hai_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5hai_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | 5hai_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5hai_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/5hai ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5hai | HTTPS FTP |
-Related structure data
Related structure data | 5hapC 5haqC 5harC 1xx2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39239.730 Da / Num. of mol.: 1 / Fragment: UNP residues 21-381 / Mutation: S64G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ampC / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P05364, beta-lactamase |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.47 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M SPG buffer (succinic acid, sodium dihydrogen phosphate, and glycine) and 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2015 |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→61.9 Å / Num. obs: 9252 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.74→2.84 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.3 / % possible all: 98.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XX2 Resolution: 2.74→61.86 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.97 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→61.86 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|