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- PDB-1px0: Crystal structure of the haloalcohol dehalogenase HheC complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1px0 | ||||||
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Title | Crystal structure of the haloalcohol dehalogenase HheC complexed with the haloalcohol mimic (R)-1-para-nitro-phenyl-2-azido-ethanol | ||||||
![]() | halohydrin dehalogenase | ||||||
![]() | LYASE / HALOALCOHOL DEHALOGENASE / HALOHYDRIN DEHALOGENASE / HALOHYDRIN HYDROGEN-HALIDE LYASE / SDR FAMILY / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / ROSSMANN FOLD | ||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / (R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL / Halohydrin dehalogenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Jong, R.M. / Tiesinga, J.J.W. / Rozeboom, H.J. / Kalk, K.H. / Tang, L. / Janssen, D.B. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: Structure and Mechanism of a Bacterial Haloalcohol Dehalogenase: a new variation of the short-chain dehydrogenase/reductase fold without an NAD(P)H binding site Authors: de Jong, R.M. / Tiesinga, J.J.W. / Rozeboom, H.J. / Kalk, K.H. / Tang, L. / Janssen, D.B. / Dijkstra, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.3 KB | Display | ![]() |
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PDB format | ![]() | 173.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.5 KB | Display | ![]() |
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Full document | ![]() | 497.6 KB | Display | |
Data in XML | ![]() | 48.9 KB | Display | |
Data in CIF | ![]() | 70.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pwxSC ![]() 1pwzC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The second part of the tetrameric biological assembly is generated by the two fold axis |
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Components
#1: Protein | Mass: 27979.666 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-RPN / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.21 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: ammonium sulfate, bis-tris buffer, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 78669 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.049 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.8 / Num. unique all: 7407 / Rsym value: 0.217 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 1029109 |
Reflection shell | *PLUS Lowest resolution: 2 Å / % possible obs: 93.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PWX Resolution: 1.9→29.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2847900.29 / Data cutoff high rms absF: 2847900.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.8007 Å2 / ksol: 0.385201 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.169 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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