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Yorodumi- PDB-3myo: Crystal structure of tagatose-1,6-bisphosphate aldolase from Stre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3myo | ||||||
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Title | Crystal structure of tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes | ||||||
Components | Tagatose 1,6-diphosphate aldolase 1 | ||||||
Keywords | LYASE / beta-alpha-barrel | ||||||
Function / homology | Function and homology information tagatose-bisphosphate aldolase / lactose catabolic process via tagatose-6-phosphate / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / tagatose-bisphosphate aldolase activity Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lee, S.J. / Kim, H.S. / Kim, D.J. / Yoon, H.J. / Kim, K.H. / Yoon, J.Y. / Suh, S.W. | ||||||
Citation | Journal: Febs Lett. / Year: 2011 Title: Crystal structures of LacD from Staphylococcus aureus and LacD.1 from Streptococcus pyogenes: Insights into substrate specificity and virulence gene regulation Authors: Lee, S.J. / Kim, H.S. / Kim, D.J. / Yoon, H.J. / Kim, K.H. / Yoon, J.Y. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3myo.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3myo.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 3myo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3myo_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 3myo_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 3myo_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 3myo_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/3myo ftp://data.pdbj.org/pub/pdb/validation_reports/my/3myo | HTTPS FTP |
-Related structure data
Related structure data | 3mypSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37118.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: serotype M1 / Gene: LACD.1, LACD1, SPY_1704, M5005_SPY1395 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P63703, tagatose-bisphosphate aldolase #2: 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: 3.98 Å3/Da / Density % sol: 69.13 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M sodium citrate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 42128 / Redundancy: 8.1 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 6.1 / Num. unique all: 4155 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MYP Resolution: 2.5→19.98 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.295 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R Free: 0.21 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.794 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.499→2.563 Å / Total num. of bins used: 20
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