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Yorodumi- PDB-5ihj: Fusion of Maltose-binding Protein and PilA from Acinetobacter bau... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ihj | |||||||||
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Title | Fusion of Maltose-binding Protein and PilA from Acinetobacter baumannii BIDMC57 | |||||||||
Components | Maltose-binding periplasmic protein,Fimbrial protein | |||||||||
Keywords | CELL ADHESION / adhesion / extracellular appendage / fimbriae | |||||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / pilus / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport ...protein secretion by the type II secretion system / type II protein secretion system complex / pilus / 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 / membrane => GO:0016020 / periplasmic space / cell adhesion / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Acinetobacter baumannii 216872 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | |||||||||
Authors | Piepenbrink, K.H. / Sundberg, E.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter. Authors: Piepenbrink, K.H. / Lillehoj, E. / Harding, C.M. / Labonte, J.W. / Zuo, X. / Rapp, C.A. / Munson, R.S. / Goldblum, S.E. / Feldman, M.F. / Gray, J.J. / Sundberg, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ihj.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ihj.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ihj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ihj_validation.pdf.gz | 849.3 KB | Display | wwPDB validaton report |
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Full document | 5ihj_full_validation.pdf.gz | 853.5 KB | Display | |
Data in XML | 5ihj_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 5ihj_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/5ihj ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ihj | 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 53044.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Acinetobacter baumannii 216872 (bacteria) Strain: K12 / Gene: malE, b4034, JW3994, tfpA, J633_2062 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: A0A140QW15 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
-Non-polymers , 4 types, 81 molecules
#3: Chemical | ChemComp-MPD / ( | ||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Bicine/Trizma pH 8.0 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.06M CaCl 0.06M MgCl 50 mM NaCl 3% EtOH |
-Data collection
Diffraction | Mean temperature: 107.1 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 21, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→50 Å / Num. obs: 23793 / % possible obs: 71.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.351 / Rpim(I) all: 0.169 / Rrim(I) all: 0.392 / Χ2: 3.498 / Net I/av σ(I): 7.056 / Net I/σ(I): 4.6 / Num. measured all: 127780 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.93 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 105.26 Å2 / Biso mean: 28.0943 Å2 / Biso min: 11.98 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.93 Å
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LS refinement shell | Resolution: 2.2→2.279 Å / Num. reflection obs: 2036 |