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Yorodumi- PDB-5fip: Discovery and characterization of a novel thermostable and highly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fip | ||||||
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Title | Discovery and characterization of a novel thermostable and highly halotolerant GH5 cellulase from an Icelandic hot spring isolate | ||||||
Components | GH5 CELLULASE | ||||||
Keywords | HYDROLASE / CELLULASE / GH5 | ||||||
Function / homology | Function and homology information cellulase activity / cellulose catabolic process / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | UNIDENTIFIED (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Zarafeta, D. / Kissas, D. / Sayer, C. / Gudbergsdottir, S.R. / Ladoukakis, E. / Isupov, M.N. / Chatziioannou, A. / Peng, X. / Littlechild, J.A. / Skretas, G. / Kolisis, F.N. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Discovery and Characterization of a Thermostable and Highly Halotolerant Gh5 Cellulase from an Icelandic Hot Spring Isolate. Authors: Zarafeta, D. / Kissas, D. / Sayer, C. / Gudbergsdottir, S.R. / Ladoukakis, E. / Isupov, M.N. / Chatziioannou, A. / Peng, X. / Littlechild, J.A. / Skretas, G. / Kolisis, F.N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fip.cif.gz | 293.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fip.ent.gz | 238.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fip_validation.pdf.gz | 788.8 KB | Display | wwPDB validaton report |
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Full document | 5fip_full_validation.pdf.gz | 816.7 KB | Display | |
Data in XML | 5fip_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 5fip_validation.cif.gz | 81.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/5fip ftp://data.pdbj.org/pub/pdb/validation_reports/fi/5fip | HTTPS FTP |
-Related structure data
Related structure data | 1g01S 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37264.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ICELANDIC HOT SPRING ISOLATE / Source: (natural) UNIDENTIFIED (others) / References: UniProt: I3VS73*PLUS, cellulase |
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-Non-polymers , 8 types, 640 molecules
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-IPA / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PG6 / | #8: Chemical | ChemComp-PG4 / | #9: 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: 2.36 Å3/Da / Density % sol: 47 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→36.38 Å / Num. obs: 126320 / % possible obs: 97.5 % / Observed criterion σ(I): 1.8 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.88→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.8 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G01 Resolution: 1.88→36.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.027 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.141 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 43.187 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→36.38 Å
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Refine LS restraints |
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