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- PDB-1tzk: Crystal structure of 1-aminocyclopropane-1-carboxylate-deaminase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tzk | |||||||||
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Title | Crystal structure of 1-aminocyclopropane-1-carboxylate-deaminase complexed with alpha-keto-butyrate | |||||||||
![]() | 1-aminocyclopropane-1-carboxylate deaminase | |||||||||
![]() | HYDROLASE / ACCD / COMPLEX / CRYSTAL / PLP / SUBSTRATE | |||||||||
Function / homology | ![]() 1-aminocyclopropane-1-carboxylate metabolic process / amine catabolic process / 1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase activity / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Karthikeyan, S. / Zhou, Q. / Zhao, Z. / Kao, C.L. / Tao, Z. / Robinson, H. / Liu, H.W. / Zhang, H. | |||||||||
![]() | ![]() Title: Structural Analysis of Pseudomonas 1-Aminocyclopropane-1-carboxylate Deaminase Complexes: Insight into the Mechanism of a Unique Pyridoxal-5'-phosphate Dependent Cyclopropane Ring-Opening Reaction Authors: Karthikeyan, S. / Zhou, Q. / Zhao, Z. / Kao, C.L. / Tao, Z. / Robinson, H. / Liu, H.W. / Zhang, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 269.4 KB | Display | ![]() |
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PDB format | ![]() | 217.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1tyzSC ![]() 1tz2C ![]() 1tzjC ![]() 1tzmC 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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Components
#1: Protein | Mass: 36714.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q00740, 1-aminocyclopropane-1-carboxylate deaminase #2: Chemical | ChemComp-PLP / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ISOPROPANOL, PEG 4000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2003 / Details: NULL |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. all: 112020 / Num. obs: 110470 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 26.1 Å2 / Rsym value: 0.077 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.52 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TYZ Resolution: 2→29.89 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2902909.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.2755 Å2 / ksol: 0.346129 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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