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Yorodumi- PDB-1tml: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF A THERMOPHILIC ENDOC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tml | ||||||
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Title | CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF A THERMOPHILIC ENDOCELLULASE | ||||||
Components | ENDO-1,4-BETA-D-GLUCANASECellulase | ||||||
Keywords | BETA-AMYLASE / ENDOCELLULASE / CATALYTIC DOMAIN | ||||||
Function / homology | Function and homology information cellulase / polysaccharide binding / cellulase activity / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Spezio, M. / Wilson, D.B. / Karplus, P.A. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Crystal structure of the catalytic domain of a thermophilic endocellulase. Authors: Spezio, M. / Wilson, D.B. / Karplus, P.A. #1: Journal: To be Published Title: Crystal Structure of the Catalytic Domain of a Thermophilic Endocellulase Authors: Spezio, M. / Wilson, D.B. / Karplus, P.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS *COR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *COR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. IN ADDITION, STRAND 1 IS BIFURCATED THUS THE BARREL IS REPRESENTED BY TWO SETS OF SHEET RECORDS *COR* AND *BOR* WHERE STRANDS 2, 3, 4, 5, 6, 7, AND 8 ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tml.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tml.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tml ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tml | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES ASN 1 AND ASP 2 ARE NOT WELL ORDERED AND HAVE VERY WEAK ELECTRON DENSITY. 2: RESIDUE TRP 162, IN THE ACTIVE SITE CLEFT, IS WELL ORDERED AND HAS STRONG DENSITY EVEN THOUGH ITS MAIN CHAIN TORSION ANGLES ARE OUTSIDE THE FAVORABLE REGIONS OF A RAMACHANDRAN PLOT. |
-Components
#1: Protein | Mass: 30436.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / References: UniProt: P26222, cellulase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | D1 AND F1 OF THE HELIX ARE SMALL AND ARE NOT EXACTLY CONSERVED BETWEEN THIS STRUCTURE AND ...D1 AND F1 OF THE HELIX ARE SMALL AND ARE NOT EXACTLY CONSERVED BETWEEN THIS STRUCTURE AND CELLOBIOHY |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.62 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 21081 / % possible obs: 97 % / Num. measured all: 79576 / Rmerge(I) obs: 0.0459 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.184 / Rfactor obs: 0.184 / Highest resolution: 1.8 Å Details: RESIDUES ASN 1 AND ASP 2 ARE NOT WELL ORDERED AND HAVE VERY WEAK ELECTRON DENSITY. RESIDUE TRP 162, IN THE ACTIVE SITE CLEFT, IS WELL ORDERED AND HAS STRONG DENSITY EVEN THOUGH ITS MAIN ...Details: RESIDUES ASN 1 AND ASP 2 ARE NOT WELL ORDERED AND HAVE VERY WEAK ELECTRON DENSITY. RESIDUE TRP 162, IN THE ACTIVE SITE CLEFT, IS WELL ORDERED AND HAS STRONG DENSITY EVEN THOUGH ITS MAIN CHAIN TORSION ANGLES ARE OUTSIDE THE FAVORABLE REGIONS OF A RAMACHANDRAN PLOT. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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