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Yorodumi- PDB-1tzj: Crystal Structure of 1-aminocyclopropane-1-carboxylate deaminase ... -
+Open data
-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 | ||||||
Components | 1-aminocyclopropane-1-carboxylate deaminase | ||||||
Keywords | HYDROLASE / ACCD / substrate / PLP / Crystal / Complex | ||||||
Function / homology | Function and homology information 1-aminocyclopropane-1-carboxylate metabolic process / amine catabolic process / 1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Karthikeyan, S. / Zhou, Q. / Zhao, Z. / Kao, C.L. / Tao, Z. / Robinson, H. / Liu, H.W. / Zhang, H. | ||||||
Citation | Journal: Biochemistry / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tzj.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tzj.ent.gz | 218.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tzj ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tzj | 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 (ref.) |
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Similar 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: 36714.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: ACP / Plasmid: PET17B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9778 Å |
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: 0.9778 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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