+Open data
-Basic information
Entry | Database: PDB / ID: 5wpz | |||||||||
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Title | Crystal structure of MNDA PYD with MBP tag | |||||||||
Components | MBP-hMNDA-PYD | |||||||||
Keywords | SUGAR BINDING PROTEIN / death fold / MBP tag / crystallization tag | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Jin, T.C. / Xiao, T.S. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Design of an expression system to enhance MBP-mediated crystallization Authors: Jin, T.C. / Chuenchor, W. / Jiang, J. / Cheng, J. / Li, Y. / Fang, K. / Huang, M. / Smith, P. / Xiao, T.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wpz.cif.gz | 549.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wpz.ent.gz | 454.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wpz_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 5wpz_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 5wpz_validation.xml.gz | 101 KB | Display | |
Data in CIF | 5wpz_validation.cif.gz | 143 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/5wpz ftp://data.pdbj.org/pub/pdb/validation_reports/wp/5wpz | HTTPS FTP |
-Related structure data
Related structure data | 5h7nC 5h7qC 5wq6C 4ifpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 52804.348 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9*PLUS #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #3: 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: 2.63 Å3/Da / Density % sol: 53.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 15% PEG 4000, 0.2M NH4Ac, 0.1M NaAc, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 201859 / % possible obs: 89 % / Redundancy: 13.6 % / CC1/2: 0.999 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 3.4 / CC1/2: 0.937 / % possible all: 53.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IFP Resolution: 2→48.361 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.361 Å
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Refine LS restraints |
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LS refinement shell |
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