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Yorodumi- PDB-7mdh: STRUCTURAL BASIS FOR LIGHT ACITVATION OF A CHLOROPLAST ENZYME. TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mdh | ||||||
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Title | STRUCTURAL BASIS FOR LIGHT ACITVATION OF A CHLOROPLAST ENZYME. THE STRUCTURE OF SORGHUM NADP-MALATE DEHYDROGENASE IN ITS OXIDIZED FORM | ||||||
Components | PROTEIN (MALATE DEHYDROGENASE) | ||||||
Keywords | CHLOROPLASTIC MALATE DEHYDROGENASE / CHLOROPLASTIC MALATE DEHYDROGENASE (NADP+) / ACTIVATED BY LIGHT | ||||||
Function / homology | Function and homology information malate dehydrogenase (NADP+) / L-malate dehydrogenase (NADP+) activity / malate metabolic process / chloroplast / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Sorghum bicolor (sorghum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Johansson, K. / Ramaswamy, S. / Saarinen, M. / Lemaire-Chamley, M. / Issakidis-Bourguet, E. / Miginiac-Maslow, M. / Eklund, H. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural basis for light activation of a chloroplast enzyme: the structure of sorghum NADP-malate dehydrogenase in its oxidized form. Authors: Johansson, K. / Ramaswamy, S. / Saarinen, M. / Lemaire-Chamley, M. / Issakidis-Bourguet, E. / Miginiac-Maslow, M. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mdh.cif.gz | 283.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mdh.ent.gz | 229.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mdh_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 7mdh_full_validation.pdf.gz | 491.1 KB | Display | |
Data in XML | 7mdh_validation.xml.gz | 54.6 KB | Display | |
Data in CIF | 7mdh_validation.cif.gz | 74.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/7mdh ftp://data.pdbj.org/pub/pdb/validation_reports/md/7mdh | HTTPS FTP |
-Related structure data
Related structure data | 1bmdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 40866.426 Da / Num. of mol.: 4 / Mutation: DELETION OF FIRST 15 N-TERMINAL RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Tissue: LEAF / Organelle: CHLOROPLAST / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17606, malate dehydrogenase (NADP+) #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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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: 2.74 Å3/Da / Density % sol: 61 % / Description: POLY-ALANINE MODEL | |||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.996 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 66459 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 30.2 Å2 / Rsym value: 0.068 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 99.8 |
Reflection | *PLUS Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 99.8 % / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BMD Resolution: 2.4→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 30748455.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.245 |