+Open data
-Basic information
Entry | Database: PDB / ID: 3mpo | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a hydrolase from Lactobacillus brevis | ||||||
Components | Predicted hydrolase of the HAD superfamily | ||||||
Keywords | HYDROLASE / SGX / PSI / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a hydrolase from Lactobacillus brevis Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mpo.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mpo.ent.gz | 165 KB | Display | PDB format |
PDBx/mmJSON format | 3mpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mpo ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mpo | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31211.818 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / JCM 1170) / Gene: HAD, LVIS_0481 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) Strain (production host): BL21 (DE3)-Codon+RIL (p)-stratagene References: UniProt: Q03T33 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.36 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 4% Tacsimate pH 4.0, 12% w/v Polythylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→130.7 Å / Num. obs: 28778 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 53.6 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 10.2 / Num. unique all: 4123 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.9→54.127 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.18 / Phase error: 28.16 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.761 Å2 / ksol: 0.299 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→54.127 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|