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Open data
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Basic information
Entry | Database: PDB / ID: 4alf | ||||||
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Title | Pseudomonas fluorescens PhoX in complex with phosphate | ||||||
![]() | ALKALINE PHOSPHATASE PHOX | ||||||
![]() | HYDROLASE / BETA-PROPELLER | ||||||
Function / homology | Alkaline phosphatase PhoX / Alkaline phosphatase PhoX / Six-bladed beta-propeller, TolB-like / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / metal ion binding / MU-OXO-DIIRON / PHOSPHATE ION / Transcriptional initiation protein Tat![]() | ||||||
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 | ![]() | 917.2 KB | Display | ![]() |
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PDB format | ![]() | 764.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zwuSC ![]() 4a9vC ![]() 4a9xC ![]() 4amfC S: Starting model for refinement C: citing same article ( |
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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: (0.083774, -0.996375, 0.014773), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64633.547 Da / Num. of mol.: 2 / Fragment: RESIDUES 48-633 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1437 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FEO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FEO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | COMPLEX WITH ORTHOPHOSPSequence details | CTERMINALL | |
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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: 0.1 M TRIS HCL PH 8.0, 0.2 M LICL, REMARK 280 20% W/V PEG 6000. THE CRYSTALS WERE SOAKED WITH 100 UL PHOSPHATE BUFFERED SALINE FOR HALF AN HOUR |
-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: 1.25→16.2 Å / Num. obs: 258332 / % possible obs: 83.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.25→1.31 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 74.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZWU Resolution: 1.25→16.14 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.4 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY. OCCUPANCY REFINEMENT IN AUTOBUSTER PRIOR TO REFMAC5 REFINEMENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→16.14 Å
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Refine LS restraints |
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