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- PDB-7zd1: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocyst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zd1 | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Hg2+ ions | ||||||
![]() | Adenosylhomocysteinase | ||||||
![]() | HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS / INHIBITION / METAL BINDING / MERCURY | ||||||
Function / homology | ![]() adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malecki, P.H. / Gawel, M. / Brzezinski, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Hg2+ ions Authors: Malecki, P.H. / Gawel, M. / Brzezinski, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 830.1 KB | Display | ![]() |
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PDB format | ![]() | 681.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6f3mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 51735.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ahcY, sahH, PA0432 / Production host: ![]() ![]() |
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-Non-polymers , 8 types, 2051 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ADN / #4: Chemical | #5: Chemical | ChemComp-PDO / #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-HG / #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.09 % / Description: 3-D plate |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.1 M bicine/Trizma base pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→105.474 Å / Num. obs: 679848 / % possible obs: 99.1 % / Redundancy: 3.437 % / Biso Wilson estimate: 32.704 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 0.864 / Net I/σ(I): 9.57 / Num. measured all: 2336708 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6F3M Resolution: 1.56→105.47 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.387 / SU ML: 0.049 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 130.63 Å2 / Biso mean: 30.917 Å2 / Biso min: 10.82 Å2
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Refinement step | Cycle: final / Resolution: 1.56→105.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.561→1.601 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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