+Open data
-Basic information
Entry | Database: PDB / ID: 4upk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Phosphonate monoester hydrolase SpPMH from Silicibacter pomeroyi | |||||||||
Components | PHOSPHONATE MONOESTER HYDROLASE | |||||||||
Keywords | HYDROLASE / ALAKALINE PHOSPHATASE SUPERFAMILY / PROMISCUITY | |||||||||
Function / homology | Function and homology information phosphorus metabolic process / phosphoric ester hydrolase activity / sulfuric ester hydrolase activity Similarity search - Function | |||||||||
Biological species | RUEGERIA POMEROYI (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | |||||||||
Authors | Valkov, E. / van Loo, B. / Hollfelder, F. / Hyvonen, M. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily. Authors: van Loo, B. / Bayer, C.D. / Fischer, G. / Jonas, S. / Valkov, E. / Mohamed, M.F. / Vorobieva, A. / Dutruel, C. / Hyvonen, M. / Hollfelder, F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4upk.cif.gz | 601.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4upk.ent.gz | 499.7 KB | Display | PDB format |
PDBx/mmJSON format | 4upk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4upk_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4upk_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 4upk_validation.xml.gz | 58.7 KB | Display | |
Data in CIF | 4upk_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upk ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upk | HTTPS FTP |
-Related structure data
Related structure data | 4uphC 4upiC 4uplC 2vqrS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 |
| |||||||||||||||
3 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 60210.281 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RUEGERIA POMEROYI (bacteria) / Strain: DSS-3 Description: GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURE (DSMZ) Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LKJ1 #2: Water | ChemComp-HOH / | Sequence details | N-TERMINAL SEQUENCE MASWSHPQFE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.8 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 0.1 M BIS-TRIS-PROPANE PH 7.0, 9% (W/V) PEG 8000, 0.2 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→19.75 Å / Num. obs: 119850 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 14.2 % / Biso Wilson estimate: 28.78 Å2 / Rmerge(I) obs: 0.39 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.24→2.28 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.6 / % possible all: 90.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VQR Resolution: 2.24→18.35 Å / Cor.coef. Fo:Fc: 0.8787 / Cor.coef. Fo:Fc free: 0.8416 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.169
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.31 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.285 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→18.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.24→2.3 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|