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Open data
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Basic information
Entry | Database: PDB / ID: 7xhz | ||||||
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Title | Crystal structure of SAV2152 from MRSA | ||||||
![]() | Phosphatase, SAV2152 | ||||||
![]() | HYDROLASE / Phosphatase | ||||||
Function / homology | Cof family / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / phosphatase activity / HAD superfamily / HAD-like superfamily / Cof-type HAD-IIB family hydrolase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, H.J. / Seok, S.H. / Kim, J.H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of SAV2152 from MRSA Authors: Park, H.J. / Seok, S.H. / Kim, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.4 KB | Display | ![]() |
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PDB format | ![]() | 120.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.4 KB | Display | ![]() |
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Full document | ![]() | 429 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
#1: Protein | Mass: 26494.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SAV2152 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 58.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 17% PEG 8000, 0.1M CAPS pH 10.5, 0.3M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→27.76 Å / Num. obs: 24669 / % possible obs: 99.91 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Net I/av σ(I): 13.3 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.92→1.98 Å / Mean I/σ(I) obs: 4.85 / Num. unique obs: 24669 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / % possible all: 99.91 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 37.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→27.76 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: 27.8237100586 Å / Origin y: 48.6700310918 Å / Origin z: 26.3773340167 Å
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Refinement TLS group | Selection details: all |