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Yorodumi- PDB-5j1d: X-ray crystal structure of Phosphate binding protein (PBP) from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j1d | ||||||
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Title | X-ray crystal structure of Phosphate binding protein (PBP) from Stenotrophomonas maltophilia | ||||||
Components | Phosphate binding protein | ||||||
Keywords | PROTEIN BINDING / Venus flytrap / ATP binding cassette / Serendipitous / Phosphate binding protein | ||||||
Function / homology | : / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / Alkaline phosphatase Function and homology information | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hatti, K. / Gulati, A. / Narayanswamy, S. / Murthy, M.R.N. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Determination of crystal structures of proteins of unknown identity using a marathon molecular replacement procedure: structure of Stenotrophomonas maltophilia phosphate-binding protein. Authors: Hatti, K. / Gulati, A. / Srinivasan, N. / Murthy, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j1d.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j1d.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 5j1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j1d_validation.pdf.gz | 424.8 KB | Display | wwPDB validaton report |
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Full document | 5j1d_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 5j1d_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 5j1d_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/5j1d ftp://data.pdbj.org/pub/pdb/validation_reports/j1/5j1d | HTTPS FTP |
-Related 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: 38240.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Stenotrophomonas maltophilia (bacteria) / References: UniProt: A0A4T1DUK4*PLUS | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-tris, pH 6.5, 20% PEG MME-5000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 29, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→55.071 Å / Num. obs: 25257 / % possible obs: 100 % / Redundancy: 4.9 % / Rsym value: 0.08 / Net I/av σ(I): 8.805 / Net I/σ(I): 16.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q9T, 2V3Q, 4F1V, 4M1V Resolution: 1.9→55.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.098 / SU ML: 0.063 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.106 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.83 Å2 / Biso mean: 8.864 Å2 / Biso min: 2.76 Å2
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Refinement step | Cycle: final / Resolution: 1.9→55.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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