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Yorodumi- PDB-1cd2: LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cd2 | ||||||
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Title | LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+ | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ONE-CARBON METABOLISM | ||||||
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 / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Pneumocystis carinii (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Blakley, R.L. / Gangjee, A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+. Authors: Cody, V. / Galitsky, N. / Rak, D. / Luft, J.R. / Pangborn, W. / Queener, S.F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Comparison of ternary complexes of Pneumocystis carinii and wild-type human dihydrofolate reductase with coenzyme NADPH and a novel classical antitumor furo[2,3-d]pyrimidine antifolate. Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Gangjee, A. / Devraj, R. / Queener, S.F. / Blakley, R.L. #2: Journal: J.Biol.Chem. / Year: 1995 Title: Methotrexate-resistant variants of human dihydrofolate reductase with substitutions of leucine 22. Kinetics, crystallography, and potential as selectable markers. Authors: Lewis, W.S. / Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Chunduru, S.K. / Spencer, H.T. / Appleman, J.R. / Blakley, R.L. #3: Journal: J.Biol.Chem. / Year: 1994 Title: Methotrexate-resistant variants of human dihydrofolate reductase. Effects of Phe31 substitutions. Authors: Chunduru, S.K. / Cody, V. / Luft, J.R. / Pangborn, W. / Appleman, J.R. / Blakley, R.L. #4: Journal: Anti-Cancer Drug Des. / Year: 1992 Title: Crystal structure determination at 2.3 A of recombinant human dihydrofolate reductase ternary complex with NADPH and methotrexate-gamma-tetrazole. Authors: Cody, V. / Luft, J.R. / Ciszak, E. / Kalman, T.I. / Freisheim, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cd2.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cd2.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 1cd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cd2_validation.pdf.gz | 538.7 KB | Display | wwPDB validaton report |
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Full document | 1cd2_full_validation.pdf.gz | 552.9 KB | Display | |
Data in XML | 1cd2_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1cd2_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/1cd2 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/1cd2 | HTTPS FTP |
-Related structure data
Related structure data | 1e26C 2cd2C 3cd2C 4cd2C 1dyrS 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: 23918.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH NADP+ AND FOLATE / Source: (gene. exp.) Pneumocystis carinii (fungus) / Plasmid: PT7-7 / Gene (production host): C-DNA P.CARINII DHFR / Production host: Escherichia coli (E. coli) / References: UniProt: P16184, dihydrofolate reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-FOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 10 ML PROTEIN, 1 MICROLITER 50MM MES, PH 6.5, 100MM KCL, 9 ML 50%(W/W)PEG 2K., pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: unknown / Details: temperature gradient | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 15, 1994 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→8 Å / Num. obs: 10428 / % possible obs: 84.7 % / Observed criterion σ(I): 2 / Redundancy: 3.09 % / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.18→2.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 2.6 / Rsym value: 33.3 / % possible all: 90.3 |
Reflection | *PLUS Highest resolution: 1.94 Å / Lowest resolution: 8 Å / % possible obs: 84.7 % / Observed criterion σ(I): 2 / Redundancy: 3.09 % |
Reflection shell | *PLUS Highest resolution: 2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DYR Resolution: 2.2→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 23.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |