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Yorodumi- PDB-5cxp: X-ray crystallographic protein structure of the glycoside hydrola... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cxp | ||||||
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Title | X-ray crystallographic protein structure of the glycoside hydrolase family 30 subfamily 8 xylanase, Xyn30A, from Clostridium acetobutylicum | ||||||
Components | Possible xylan degradation enzyme (Glycosyl hydrolase family 30-like domain and Ricin B-like domain) | ||||||
Keywords | HYDROLASE / glycoside hydrolase family 30 subfamily 8 / xylanase / clostridium acetobutylicum / (beta/alpha)8 + beta protein fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | St John, F.J. / Pozharski, E. / Hurlbert, J.C. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a GH30 xylanase Authors: St John, J.F. / Dietrich, D. / Bologna, P. / Hurlbert, J.C. / Pozharski, E.P. / Crooks, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cxp.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cxp.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cxp_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5cxp_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5cxp_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 5cxp_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/5cxp ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cxp | HTTPS FTP |
-Related structure data
Related structure data | 3kl3S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42622.441 Da / Num. of mol.: 1 / Fragment: UNP residues 32-418 Source method: isolated from a genetically manipulated source Details: pSOL1 natural plasmid Source: (gene. exp.) Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (bacteria) Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Gene: CA_P0119 / Plasmid: pET28 / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): DH5[alpha] / References: UniProt: Q97TI2 | ||||||
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#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-P6G / #5: 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: 3.11 Å3/Da / Density % sol: 60.4 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: JCSG condition D6: 0.1M HEPES pH 7.5, 4.3 M NaCl |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→30 Å / Num. obs: 51748 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.256 / Net I/σ(I): 6.82 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.02 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KL3 Resolution: 1.77→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.126 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 16.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→30 Å
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Refine LS restraints |
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