+Open data
-Basic information
Entry | Database: PDB / ID: 1drv | ||||||
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Title | ESCHERICHIA COLI DHPR/ACNADH COMPLEX | ||||||
Components | DIHYDRODIPICOLINATE REDUCTASE4-hydroxy-tetrahydrodipicolinate reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / amino acid biosynthetic process / NAD binding / NADP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Reddy, S.G. / Scapin, G. / Blanchard, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes. Authors: Reddy, S.G. / Scapin, G. / Blanchard, J.S. #1: Journal: Biochemistry / Year: 1995 Title: Three-Dimensional Structure of Escherichia Coli Dihydrodipicolinate Reductase Authors: Scapin, G. / Blanchard, J.S. / Sacchettini, J.C. #2: Journal: Biochemistry / Year: 1995 Title: Expression, Purification, and Characterization of Escherichia Coli Dihydrodipicolinate Reductase Authors: Reddy, S.G. / Sacchettini, J.C. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1drv.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1drv.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 1drv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/1drv ftp://data.pdbj.org/pub/pdb/validation_reports/dr/1drv | HTTPS FTP |
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-Related 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: 28793.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DAPB / Plasmid: PET3D / Gene (production host): DAPB / Production host: Escherichia coli (E. coli) / Strain (production host): BL213D / References: UniProt: P04036, EC: 1.3.1.26 |
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#2: Chemical | ChemComp-A3D / |
#3: 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: 2.8 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 2.2 M (NH4)2SO4 IN 100 MM HEPES, PH=7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Scapin, G., (1995) Biochemistry, 34, 3502. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 26, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 14402 / % possible obs: 87.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.277 / % possible all: 78.1 |
Reflection | *PLUS % possible obs: 87.3 % / Rmerge(I) obs: 0.094 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DHPR-NADPH COMPLEX Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL.DAT / σ(F): 2 Stereochemistry target values: ENGH AND HUBER MODIFIED FOR TNT
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Solvent computation | Bsol: 742.8 Å2 / ksol: 1.1 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 14483 / Rfactor all: 0.196 / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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