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Yorodumi- PDB-3clm: Crystal structure of transaldolase (YP_208650.1) from Neisseria g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3clm | ||||||
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Title | Crystal structure of transaldolase (YP_208650.1) from Neisseria gonorrhoeae FA 1090 at 1.14 A resolution | ||||||
Components | Transaldolase | ||||||
Keywords | LYASE / YP_208650.1 / transaldolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Transferase | ||||||
Function / homology | Function and homology information transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of transaldolase (YP_208650.1) from Neisseria gonorrhoeae FA 1090 at 1.14 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3clm.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3clm.ent.gz | 133.6 KB | Display | PDB format |
PDBx/mmJSON format | 3clm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3clm_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 3clm_full_validation.pdf.gz | 444.6 KB | Display | |
Data in XML | 3clm_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 3clm_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/3clm ftp://data.pdbj.org/pub/pdb/validation_reports/cl/3clm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | AUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTED BY ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY LEADS TO THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. |
-Components
#1: Protein | Mass: 37786.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA 1090 / Gene: YP_208650.1, tal, NGO1610 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5F6E9, transaldolase | ||||
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#2: Chemical | ChemComp-CL / | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.14→29.579 Å / Num. obs: 107548 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 6.167 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.68 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.14→29.579 Å / Num. parameters: 29682 / Num. restraintsaints: 121313 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER Details: 1. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.2%. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.2%. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 1,2-ETHANEDIOL MOLECULES, A SULFATE ION FROM THE CRYSTALLIZATION CONDITIONS AND A CHLORIDE ION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.882 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→29.579 Å
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Refine LS restraints |
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