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- PDB-1hqs: CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE FROM BACILLUS SUBTILIS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hqs | ||||||
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Title | CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE FROM BACILLUS SUBTILIS | ||||||
![]() | ISOCITRATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / glyoxylate bypass / BsIDH / tricarboxylic acid cycle / protein phosphorylation / NADP | ||||||
Function / homology | ![]() isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, S.K. / Matsuno, K. / LaPorte, D.C. / Banaszak, L.J. | ||||||
![]() | ![]() Title: Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase. Authors: Singh, S.K. / Matsuno, K. / LaPorte, D.C. / Banaszak, L.J. | ||||||
History |
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Remark 600 | HETEROGEN Cys118 from both monomers have been modified with beta-mercaptoethanol. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193 KB | Display | ![]() |
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PDB format | ![]() | 152.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3icdS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 46544.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P39126, isocitrate dehydrogenase (NADP+) #2: Chemical | #3: Chemical | ChemComp-PGO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 44.38 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 23% PEG 4000, 18% propylene glycol, 0.1 M citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: APS-1 / Detector: CCD / Date: Feb 6, 1998 / Details: vertically focusing mirror |
Radiation | Monochromator: Sagitally focusing crystal/double crystal monochromator Si-111 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→99 Å / Num. all: 244628 / Num. obs: 114797 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.13 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.321 / Num. unique all: 6004 / % possible all: 46.6 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. measured all: 244628 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ICD Resolution: 1.55→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Used bulk-solvent correction. Citrate is bound in the active site of both monomers. However, the O5 and O6 atoms of the citrate bound in monomer B (res. number 825) have been set to zero to ...Details: Used bulk-solvent correction. Citrate is bound in the active site of both monomers. However, the O5 and O6 atoms of the citrate bound in monomer B (res. number 825) have been set to zero to account for a small negative peak (-3.4sigma) that appeared on them late in refinement. There are 23 pairs of water molecules less than 2.5-A apart enveloped in electron density that resembles a peanut shell or dumbbell. Their occupancies have been set to 0.5. In addition, there are 3 sets of water triplets less than 2.5-A apart enveloped in electron density that resembles a boomerang. Their occupancies have been set to 0.33. All 55 of these waters are appended at the end of the coordinate file. There is no visible electron density beyond the beta-carbon of Met1, Gln3, and Asn11 in monomer A. Their side chains were generated in O using the most common rotamers and their occupancies have been set to 0.0
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Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.202 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.324 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.326 |