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Yorodumi- PDB-2zza: Moritella profunda Dihydrofolate reductase complex with NADP+ and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zza | ||||||
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Title | Moritella profunda Dihydrofolate reductase complex with NADP+ and Folate | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / Dihydrofolate reductase / Folic acid / NADP / deep-sea / high pressure / low temperature / Moritella profunda / piezophilic / psychrophilic / psychropiezophilic | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Moritella profunda (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hata, K. / Tanaka, T. / Murakami, C. / Ohmae, E. / Gekko, K. / Shiro, Y. / Akasaka, K. | ||||||
Citation | Journal: To be Published Title: Moritella profunda Dihydrofolate reductase complex with NADP+ and Folate Authors: Hata, K. / Tanaka, T. / Murakami, C. / Ohmae, E. / Gekko, K. / Shiro, Y. / Akasaka, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zza.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zza.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zza_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2zza_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2zza_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 2zza_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/2zza ftp://data.pdbj.org/pub/pdb/validation_reports/zz/2zza | HTTPS FTP |
-Related structure data
Related structure data | 1ddsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18276.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moritella profunda (bacteria) / Strain: 2674T / Gene: dyrA / Plasmid: pUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q70YQ6, dihydrofolate reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | Sequence details | AUTHOR STATED THE FIRST RESIDUE OF THE PROTEIN IS VAL. | |
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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: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M Ammonium acetate, 0.1M sodium citrate, 15% PEG4000, 0.1 Hexammine Cobalt (III) chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 13, 2007 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 21062 / Num. obs: 21062 / % possible obs: 85.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.073 / Net I/σ(I): 2.82 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.82 / Num. unique all: 21062 / Rsym value: 0.299 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DDS Resolution: 2→31.33 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.935 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 60.12 Å2 / Biso mean: 26.807 Å2 / Biso min: 11.36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→31.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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