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- PDB-1ocm: THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 COVALENTLY COMPLEXED WIT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ocm | |||||||||
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Title | THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 COVALENTLY COMPLEXED WITH PYROPHOSPHATE FROM BRADYRHIZOBIUM JAPONICUM | |||||||||
![]() | MALONAMIDASE E2 | |||||||||
![]() | AMIDASE / MALONAMIDASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shin, S. / Ha, N.-C. / Lee, T.-H. / Oh, B.-H. | |||||||||
![]() | ![]() Title: Characterization of a Novel Ser-Cisser-Lys Catalytic Triad in Comparison with the Classical Ser-His-Asp Triad. Authors: Shin, S. / Yun, Y.S. / Koo, H.M. / Kim, Y.S. / Choi, K.Y. / Oh, B.-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 | ![]() | 180.3 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384.8 KB | Display | ![]() |
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Full document | ![]() | 399.5 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o9nC ![]() 1o9oC ![]() 1o9pC ![]() 1o9qC ![]() 1obiC ![]() 1objC ![]() 1obkC ![]() 1oblC ![]() 1ochC ![]() 1ockC ![]() 1oclC ![]() 1gr8 C: citing same article ( S: Starting model for refinement |
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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: 43591.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PYROPHOSPHATE COVALENTLY BONDED WITH RESIDUE 155 IN CHAIN A, B Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | POP A1155,B1155 PYROPHOSPH | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39.9 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 20% POLYETHYLENE GLYCOL 1000, 100 MM TRIS, PH 7.0, 10 MM PHENYLPHOSPHORODIAMIDATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / 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: MACSCIENCE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 621134 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.054 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.95 / Rsym value: 0.239 / % possible all: 87.5 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 87.5 % / Rmerge(I) obs: 0.239 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GR8 ![]() 1gr8 Resolution: 1.9→30 Å / Rfactor Rfree error: 7.9E-5 / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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