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Yorodumi- PDB-3r12: Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r12 | |||||||||
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Title | Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.75 A resolution | |||||||||
Components | Deoxyribose-phosphate aldolase | |||||||||
Keywords | LYASE / TIM BETA/ALPHA-BARREL / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | |||||||||
Function / homology | Function and homology information deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: To be published Title: Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.75 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 | 3r12.cif.gz | 211.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r12.ent.gz | 173.9 KB | Display | PDB format |
PDBx/mmJSON format | 3r12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/3r12 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/3r12 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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-Components
#1: Protein | Mass: 29159.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: deoC, TM1559, TM_1559 / Plasmid: MH1 / Production host: Escherichia Coli (E. coli) / Strain (production host): DL41 / References: UniProt: Q9X1P5, deoxyribose-phosphate aldolase #2: Chemical | #3: Chemical | ChemComp-PGO / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.02 Å3/Da / Density % sol: 39.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 25.0% 1,2-propanediol, 10.0% Glycerol, 5.0% PEG-3000, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.918370,0.977757 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2002 / Details: FLAT MIRROR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SINGLE CRYSTAL SI(311) BENT / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→47.226 Å / Num. obs: 40637 / % possible obs: 86.2 % / Observed criterion σ(I): -3 / Redundancy: 3.56 % / Biso Wilson estimate: 16.819 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.91 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→47.226 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.903 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CITRATE (CIT) AND GLYCEROL (GOL) MODELED IN THE STRUCTURE ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. ATOM RECORD CONTAINS SUM ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CITRATE (CIT) AND GLYCEROL (GOL) MODELED IN THE STRUCTURE ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.14 Å2 / Biso mean: 22.0715 Å2 / Biso min: 4.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→47.226 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 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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