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Yorodumi- PDB-3odp: Crystal structure of a putative tagatose-6-phosphate ketose/aldos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3odp | ||||||
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Title | Crystal structure of a putative tagatose-6-phosphate ketose/aldose isomerase (NT01CX_0292) from CLOSTRIDIUM NOVYI NT at 2.35 A resolution | ||||||
Components | putative tagatose-6-phosphate ketose/aldose isomerase | ||||||
Keywords | ISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information carbohydrate derivative metabolic process / carbohydrate derivative binding / isomerase activity / hydrolase activity Similarity search - Function | ||||||
Biological species | Clostridium novyi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD, molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative tagatose-6-phosphate ketose/aldose isomerase (NT01CX_0292) from CLOSTRIDIUM NOVYI NT at 2.35 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 | 3odp.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3odp.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 3odp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/3odp ftp://data.pdbj.org/pub/pdb/validation_reports/od/3odp | HTTPS FTP |
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-Related structure data
Related structure data | 3i0zS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 44513.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium novyi (bacteria) / Strain: NT / Gene: NT01CX_0292 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0Q2D8 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.42 % Description: AN INITIAL SUBSTRUCTURE SOLUTION WAS FOUND USING SHELXD AND SAD PHASES WERE REFINED WITH AUTOSHARP. AN ITERATIVE RESOLVE RUN WAS ABLE TO TRACE ~70% OF THE STRUCTURE. HOWEVER, THE ...Description: AN INITIAL SUBSTRUCTURE SOLUTION WAS FOUND USING SHELXD AND SAD PHASES WERE REFINED WITH AUTOSHARP. AN ITERATIVE RESOLVE RUN WAS ABLE TO TRACE ~70% OF THE STRUCTURE. HOWEVER, THE CONNECTIVITY OF THE RESULTING MODEL WAS POOR. MOLECULAR REPLACEMENT WITH MOLREP USING 3I0Z AS THE SEARCH MODEL PROVIDED A MORE COMPLETE STARTING MODEL FOR SUBSEQUENT MODEL BUILDING AND REFINEMENT. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50.00% PEG-200, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97871 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97871 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→77.391 Å / Num. all: 23656 / Num. obs: 23656 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 57.921 Å2 / Rsym value: 0.084 / Net I/σ(I): 12.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.01 / Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD, molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: SAD, MOLECULAR REPLACEMENT Starting model: PDB entry 3I0Z Resolution: 2.35→77.391 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 26.475 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. PEG-200 (PG4) FRAGMENTS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 7. ASSIGNMENT OF PHOSPHATE ION (PO4) WAS BASED ON ELECTRON DENSITY AND CONSERVATION OF THE BINDING SITE IN 3I0Z AND OTHER HOMOLOG STRUCTURES. 8. THE TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 9. THE RAMACHANDRAN OUTLIER RESIDUES 16 AND 308 ARE IN POOR DENSITY REGION.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 165.11 Å2 / Biso mean: 89.0472 Å2 / Biso min: 46.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→77.391 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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