+
Open data
-
Basic information
Entry | Database: PDB / ID: 1shv | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF SHV-1 BETA-LACTAMASE | ||||||
![]() | PROTEIN (BETA-LACTAMASE SHV-1) | ||||||
![]() | HYDROLASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT BINDING / DRUG DESIGN | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A. / Bonomo, R.A. / Knox, J.R. | ||||||
![]() | ![]() Title: Structure of the SHV-1 beta-lactamase. Authors: Kuzin, A.P. / Nukaga, M. / Nukaga, Y. / Hujer, A.M. / Bonomo, R.A. / Knox, J.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 66.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 466.3 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xpbS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28907.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 1 DETERGENT MOLECULE (CYMAL-6) BOUND NON-COVALENTLY Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): DH10B References: UniProt: P14557, UniProt: P0AD64*PLUS, beta-lactamase | ||
---|---|---|---|
#2: Chemical | ChemComp-MA4 / | ||
#3: Water | ChemComp-HOH / | ||
Nonpolymer details | DETERGENT USED IN CRYSTALLIZSequence details | WE USE A CONSENSUS NUMBERING IN WHICH 239 AND 253 ARE NOT USED FOR THIS ENZYME. HERE, 238 AND 240 ...WE USE A CONSENSUS NUMBERING IN WHICH 239 AND 253 ARE NOT USED FOR THIS ENZYME. HERE, 238 AND 240 ARE LINKED, AS ARE 252 AND 254. TER ARG: NUMBERING FOR THE MATURE PROTEIN STARTS AT 26 (USING A CONSENSUS CONVENTION | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: VAPOR DIFFUSION, WITH 2MG/ML PROTEIN IN 15% PEG6000, 50MM HEPES PH7.0 0.65MM CYMAL-6, OVER 30% PEG RESERVOIR AT ROOM TEMPERATURE | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→43 Å / Num. obs: 49725 / % possible obs: 0.85 % / Redundancy: 3.3 % / Rsym value: 0.065 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.96→2.09 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.194 / % possible all: 0.4 |
Reflection | *PLUS Num. obs: 15082 / % possible obs: 85 % / Num. measured all: 49725 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 40 % / Num. unique obs: 1156 / Num. measured obs: 2259 / Rmerge(I) obs: 0.194 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1XPB Resolution: 1.98→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: NO IDEAL GEOMETRY FOR DETERGENT MOLECULE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.205 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.98→2.06 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|