+Open data
-Basic information
Entry | Database: PDB / ID: 7bni | ||||||
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Title | Complex structure of SH3b domain with 2-hydroxybenzoic acid | ||||||
Components | Lysostaphin | ||||||
Keywords | CELL ADHESION / CELL WALL TARGETING/BINDING / CWT / SH3 / COMPLEX / 2-hydroxybenzoic acid / Staphylococcus simulans | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus simulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Malecki, P.H. / Sabala, I. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Complex structure of SH3b domain with 2-hydroxybenzoic acid Authors: Malecki, P.H. / Sabala, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bni.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bni.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/7bni ftp://data.pdbj.org/pub/pdb/validation_reports/bn/7bni | HTTPS FTP |
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-Related structure data
Related structure data | 5leoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10819.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus simulans (bacteria) / Gene: HMPREF3215_01322 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A133QQ41, lysostaphin #2: Chemical | ChemComp-SAL / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 6.5 Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% PEG 5K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.31→36.684 Å / Num. obs: 46043 / % possible obs: 97.4 % / Redundancy: 4.953 % / Biso Wilson estimate: 20.774 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.058 / Χ2: 0.916 / Net I/σ(I): 15.18 / Num. measured all: 228042 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LEO Resolution: 1.31→18.81 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.56 / Stereochemistry target values: ML
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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 max: 59.91 Å2 / Biso mean: 21.2445 Å2 / Biso min: 9.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.31→18.81 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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