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- PDB-4amf: Pseudomonas fluorescens PhoX in complex with the substrate analog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4amf | |||||||||
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Title | Pseudomonas fluorescens PhoX in complex with the substrate analogue AppCp | |||||||||
![]() | PHOX | |||||||||
![]() | HYDROLASE / ALKALINE PHOSPHATASE / PHOX / BETA- PROPELLER / IRON / APPCP / SUBSTRATE ANALOGUE / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yong, S.C. / Roversi, P. / Lillington, J.E.D. / Zeldin, O.B. / Garman, E.F. / Lea, S.M. / Berks, B.C. | |||||||||
![]() | ![]() Title: A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry Authors: Yong, S.C. / Roversi, P. / Lillington, J. / Rodriguez, F. / Krehenbrink, M. / Zeldin, O.B. / Garman, E.F. / Lea, S.M. / Berks, B.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 470.8 KB | Display | ![]() |
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PDB format | ![]() | 384.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 52.7 KB | Display | |
Data in CIF | ![]() | 82.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zwuC ![]() 4a9vC ![]() 4a9xSC ![]() 4alfC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.084252, -0.996433, 0.004791), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64304.242 Da / Num. of mol.: 2 / Fragment: YES Source method: isolated from a genetically manipulated source Details: COMPLEX WITH APPCP / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 1248 molecules ![](data/chem/img/ACP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FEO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FEO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-LI / | #5: Chemical | ChemComp-CA / #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | HIS-TAGGED AT THE C-TERMINUS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 8 Details: 19% PEG 6000, 0.1 M TRIS PH 7.9, 0.2 M LICL, 300 UM CACL2, SOAKED IN APPCP 1MM |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→70.38 Å / Num. obs: 166380 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.52→1.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.2 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4A9X Resolution: 1.52→67.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.07 / Details: REMARK 3 NULL
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Displacement parameters | Biso mean: 18.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.143 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→67.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.56 Å / Total num. of bins used: 20
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