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- PDB-4pmz: Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pmz | |||||||||
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Title | Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylobiose | |||||||||
![]() | Xylanase | |||||||||
![]() | HYDROLASE / xylanase | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Santos, C.R. / Martins, V.P.M. / Zanphorlin, L.M. / Ruller, R. / Murakami, M.T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanisms associated with xylan degradation by xanthomonas plant pathogens. Authors: Santos, C.R. / Hoffmam, Z.B. / de Matos Martins, V.P. / Zanphorlin, L.M. / de Paula Assis, L.H. / Honorato, R.V. / Lopes de Oliveira, P.S. / Ruller, R. / Murakami, M.T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.5 KB | Display | ![]() |
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PDB format | ![]() | 217.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pmuC ![]() 4pmvC ![]() 4pmxSC ![]() 4pmyC ![]() 4pn2C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 34199.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 306 / Gene: xynB, XAC4254 / Production host: ![]() ![]() #2: Polysaccharide | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Polyethylene glycol 8,000 / PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→42.4 Å / Num. obs: 206127 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 2.18 % / Biso Wilson estimate: 19.79 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.072 / Χ2: 1.378 / Net I/σ(I): 10.86 / Num. measured all: 438738 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PMX Resolution: 1.401→42.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.373 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.24 Å2 / Biso mean: 14.922 Å2 / Biso min: 8.36 Å2
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Refinement step | Cycle: final / Resolution: 1.401→42.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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