[English] 日本語
Yorodumi- PDB-4axh: Structure and mechanism of the first inverting alkylsulfatase spe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4axh | ||||||
---|---|---|---|---|---|---|---|
Title | Structure and mechanism of the first inverting alkylsulfatase specific for secondary alkylsulfatases | ||||||
Components | SEC-ALKYLSULFATASE | ||||||
Keywords | HYDROLASE / REACTION MECHANISM / ZINC-DEPENDENT | ||||||
Function / homology | Function and homology information (R)-specific secondary-alkylsulfatase (type III) / linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / protein dimerization activity / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS SP. DSM 6611 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Knaus, T. / Schober, M. / Faber, K. / Macheroux, P. / Wagner, U.G. | ||||||
Citation | Journal: FEBS J. / Year: 2012 Title: Structure and Mechanism of an Inverting Alkylsulfatase from Pseudomonas Sp. Dsm6611 Specific for Secondary Alkylsulfates. Authors: Knaus, T. / Schober, M. / Kepplinger, B. / Faccinelli, M. / Pitzer, J. / Faber, K. / Macheroux, P. / Wagner, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4axh.cif.gz | 255.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4axh.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 4axh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4axh_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4axh_full_validation.pdf.gz | 488.5 KB | Display | |
Data in XML | 4axh_validation.xml.gz | 46 KB | Display | |
Data in CIF | 4axh_validation.cif.gz | 63.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/4axh ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4axh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.42219, 0.471121, -0.774468), Vector: |
-Components
#1: Protein | Mass: 73979.016 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-660 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS SP. DSM 6611 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: F8KAY7 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.18076 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 21, 2009 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→19.93 Å / Num. obs: 36072 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 65.35 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.7→8.54 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.7→19.59 Å / Cor.coef. Fo:Fc: 0.9211 / Cor.coef. Fo:Fc free: 0.8849 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377 Details: B32-B193, B261-B308, B336-B37 DEFINED AND WERE MODELLED AS NCS-MATES FROM MOLECULE A. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ...Details: B32-B193, B261-B308, B336-B37 DEFINED AND WERE MODELLED AS NCS-MATES FROM MOLECULE A. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10041. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4. FOR ATOMS IN HIGHLY DISORDERED REGIONS AN OCCUPANCY OF 0.5 WAS CHOOSEN.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.443 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.78 Å / Total num. of bins used: 18
|