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- PDB-1erz: CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1erz | ||||||
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Title | CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES | ||||||
![]() | N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE | ||||||
![]() | HYDROLASE / four-layer sandwich | ||||||
Function / homology | ![]() N-carbamoyl-D-amino-acid hydrolase / N-carbamoyl-D-amino acid hydrolase activity / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nakai, T. / Hasegawa, T. / Yamashita, E. / Yamamoto, M. / Kumasaka, T. / Ueki, T. / Nanba, H. / Ikenaka, Y. / Takahashi, S. / Sato, M. / Tsukihara, T. | ||||||
![]() | ![]() Title: Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases. Authors: Nakai, T. / Hasegawa, T. / Yamashita, E. / Yamamoto, M. / Kumasaka, T. / Ueki, T. / Nanba, H. / Ikenaka, Y. / Takahashi, S. / Sato, M. / Tsukihara, T. #1: ![]() Title: Isolation of Agrobacterium sp. Strain KNK712 that Produces N-carbamyl-D-amino acid Amidohydrolase, Cloning of the Gene for this Enzyme, and Properties of the Enzyme. Authors: Nanba, H. / Ikenaka, Y. / Yamada, Y. / Yajima, K. / Takano, M. / Takahashi, S. #2: ![]() Title: Crystals and Three-dimensional Structure of DCase, and their Use Authors: Nakai, T. / Morikawa, S. / Ishii, K. / Nanba, H. / Yajima, K. / Ikenaka, Y. / Takahashi, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.9 KB | Display | ![]() |
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PDB format | ![]() | 114.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429 KB | Display | ![]() |
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Full document | ![]() | 434.8 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 48.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 on special symmetry positions |
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Details | The biological assembly is a tetramer constructed from chain A and B. A symmetry partner generated by the two-fold. |
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Components
#1: Protein | Mass: 34199.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P60327, N-carbamoyl-D-amino-acid hydrolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.35 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 6000, lithium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 13, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9341 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→69 Å / Num. all: 68606 / Num. obs: 68596 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.87 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.207 / Num. unique all: 6418 / % possible all: 91.4 |
Reflection | *PLUS Num. measured all: 189832 |
Reflection shell | *PLUS % possible obs: 91.4 % |
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Processing
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Refinement | Resolution: 1.7→69 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→69 Å
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Refine LS restraints |
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