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Yorodumi- PDB-7zd3: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocyst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zd3 | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS / INHIBITION / METAL BINDING / ZINC | ||||||
Function / homology | Function and homology information adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Malecki, P.H. / Gawel, M. / Brzezinski, K. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions Authors: Malecki, P.H. / Gawel, M. / Brzezinski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zd3.cif.gz | 984.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zd3.ent.gz | 675.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zd3_validation.pdf.gz | 11.8 MB | Display | wwPDB validaton report |
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Full document | 7zd3_full_validation.pdf.gz | 11.8 MB | Display | |
Data in XML | 7zd3_validation.xml.gz | 85 KB | Display | |
Data in CIF | 7zd3_validation.cif.gz | 128.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/7zd3 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zd3 | HTTPS FTP |
-Related structure data
Related structure data | 6f3mS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q9I685, adenosylhomocysteinase |
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-Non-polymers , 11 types, 1997 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ADN / #4: Chemical | ChemComp-BU1 / #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-ZN / #8: Chemical | ChemComp-BCN / | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-CL / | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % / 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: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 28, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→81.284 Å / Num. obs: 183152 / % possible obs: 96.3 % / Redundancy: 3.838 % / Biso Wilson estimate: 32.775 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.152 / Χ2: 0.839 / Net I/σ(I): 7.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F3M Resolution: 1.9→29.53 Å / SU ML: 0.2736 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1183 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 27.541940635 Å / Origin y: -16.6388896069 Å / Origin z: 26.4880594995 Å
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Refinement TLS group | Selection details: all |