+Open data
-Basic information
Entry | Database: PDB / ID: 3zss | ||||||
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Title | Apo form of GlgE isoform 1 from Streptomyces coelicolor | ||||||
Components | PUTATIVE GLUCANOHYDROLASE PEP1A | ||||||
Keywords | HYDROLASE / ALPHA-GLUCAN BIOSYNTHESIS / GLYCOSIDE HYDROLASE FAMILY 13_3 | ||||||
Function / homology | Function and homology information starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / oligosaccharide catabolic process / alpha-amylase activity Similarity search - Function | ||||||
Biological species | STREPTOMYCES COELICOLOR (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Syson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure of a Streptomyces Maltosyltransferase Glge: A Homologue of a Genetically Validated Anti-Tuberculosis Target. Authors: Syson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" 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 "BE" 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 "CE" 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 "DE" 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 | 3zss.cif.gz | 970.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zss.ent.gz | 810.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zss_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 3zss_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 3zss_validation.xml.gz | 85.5 KB | Display | |
Data in CIF | 3zss_validation.cif.gz | 122.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zss ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zss | HTTPS FTP |
-Related structure data
Related structure data | 3zstSC 3zt5C 3zt6C 3zt7C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 15 - 663 / Label seq-ID: 35 - 683
NCS ensembles :
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-Components
#1: Protein | Mass: 77564.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: M145 / Plasmid: PET15B-GLGE1-M145 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: Q9L1K2, Transferases; Glycosyltransferases; Hexosyltransferases, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Water | ChemComp-HOH / | Sequence details | INCLUDES AN ADDITIONAL | |
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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: 3.24 Å3/Da / Density % sol: 63 % / Description: DATA WERE HEMIHEDRALLY TWINNED |
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Crystal grow | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9709 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2010 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9709 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.8→53.15 Å / Num. obs: 351739 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 72.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZST Resolution: 1.8→314.44 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.559 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→314.44 Å
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Refine LS restraints |
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