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- PDB-3n2c: Crystal structure of prolidase eah89906 complexed with n-methylph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n2c | |||||||||
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Title | Crystal structure of prolidase eah89906 complexed with n-methylphosphonate-l-proline | |||||||||
![]() | PROLIDASE | |||||||||
![]() | HYDROLASE / UNKNOWN SOURCE / AMIDOHYDROLASE / SARGASSO SEA / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / PROLIDASE / NYSGXRC / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS | |||||||||
Function / homology | ![]() hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | UNIDENTIFIED (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Patskovsky, Y. / Xu, C. / Sauder, J.M. / Burley, S.K. / Raushel, F.M. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | |||||||||
![]() | ![]() Title: Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily . Authors: Xiang, D.F. / Patskovsky, Y. / Xu, C. / Fedorov, A.A. / Fedorov, E.V. / Sisco, A.A. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Raushel, F.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 980.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 603.6 KB | Display | ![]() |
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Full document | ![]() | 694 KB | Display | |
Data in XML | ![]() | 208.4 KB | Display | |
Data in CIF | ![]() | 277.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3feqSC ![]() 3mkvC ![]() 3mtwC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44993.988 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) UNIDENTIFIED (others) / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-LWY / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.19 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: 8% PEG8000, MES, PH 6.0, 200MM SODIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 186340 / % possible obs: 98.3 % / Observed criterion σ(I): -5 / Redundancy: 1.9 % / Biso Wilson estimate: 76.32 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 0.5 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3FEQ Resolution: 2.81→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 21.786 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.979 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.806→2.879 Å / Total num. of bins used: 20
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