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Yorodumi- PDB-1z5u: Crystal structure of S. typhimurium AphA complexed with cyclic-AMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z5u | ||||||
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Title | Crystal structure of S. typhimurium AphA complexed with cyclic-AMP | ||||||
Components | AphA protein | ||||||
Keywords | HYDROLASE / Class-B bacterial acid phosphatase / cyclic-AMP complex of AphA protein / metalloenzyme | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Makde, R.D. / Kumar, V. | ||||||
Citation | Journal: To be Published Title: Structure and Function of class-B bacterial non-specific acid phosphatase: functional role of invariant Lys154 Authors: Makde, R.D. / Gupta, G.D. / Kumar, V. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Expression, purification, crystallization and preliminary X-ray diffraction studies of recombinant class B non-specific acid phosphatase of Salmonella typhimurium Authors: Makde, R.D. / Kumar, V. / Gupta, G.D. / Jasti, J. / Singh, T.P. / Mahajan, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z5u.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z5u.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 1z5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z5u_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1z5u_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1z5u_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 1z5u_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/1z5u ftp://data.pdbj.org/pub/pdb/validation_reports/z5/1z5u | HTTPS FTP |
-Related structure data
Related structure data | 1z5gS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23870.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: aphA / Plasmid: pET21(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 56694136, UniProt: Q540U1*PLUS, acid phosphatase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CMP / #4: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: PEG6000, magnesium chloride, glycerol, sodium actetate, cyclic-AMP, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 19, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 38398 / Num. obs: 38398 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.081 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.3→2.42 Å / % possible obs: 96.2 % / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5619 / Rsym value: 0.269 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB CODE 1Z5G Resolution: 2.3→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Flat Model / Bsol: 32.18 Å2 / ksol: 0.311 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2 | |||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 10
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Xplor file |
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