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- PDB-1tzj: Crystal Structure of 1-aminocyclopropane-1-carboxylate deaminase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tzj | ||||||
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Title | Crystal Structure of 1-aminocyclopropane-1-carboxylate deaminase complexed with d-vinyl glycine | ||||||
![]() | 1-aminocyclopropane-1-carboxylate deaminase![]() | ||||||
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Function / homology | ![]() 1-aminocyclopropane-1-carboxylate metabolic process / amine catabolic process / ![]() ![]() ![]() 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 | ![]() | 270.1 KB | Display | ![]() |
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PDB format | ![]() | 218.1 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 ![]() 1tzkC ![]() 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, ![]() #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: 56.53 % |
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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: Jun 20, 2003 / Details: NULL |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.97→30 Å / Num. all: 110952 / Num. obs: 110765 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 28.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 44.5 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 9.2 / Rsym value: 0.36 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1TYZ Resolution: 1.99→29.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2775039.51 / 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: 54.6806 Å2 / ksol: 0.344591 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.99→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.11 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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