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Yorodumi- PDB-4jca: Crystal Structure of the apo form of the evolved variant of the c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jca | ||||||
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Title | Crystal Structure of the apo form of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1. Northeast Structural Genomics Consortium (NESG) Target OR273 | ||||||
Components | serine hydrolase | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) | ||||||
Function / homology | Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / CITRIC ACID / RUBIDIUM ION Function and homology information | ||||||
Biological species | artificial gene (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.411 Å | ||||||
Authors | Kuzin, A.P. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Tong, S. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. ...Kuzin, A.P. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Tong, S. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 Title: Design of activated serine-containing catalytic triads with atomic-level accuracy. Authors: Rajagopalan, S. / Wang, C. / Yu, K. / Kuzin, A.P. / Richter, F. / Lew, S. / Miklos, A.E. / Matthews, M.L. / Seetharaman, J. / Su, M. / Hunt, J.F. / Cravatt, B.F. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jca.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jca.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 4jca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jca_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 4jca_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 4jca_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4jca_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/4jca ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jca | HTTPS FTP |
-Related structure data
Related structure data | 3tp4C 3v45C 4drtC 4essC 4etjSC 4etkC 4f2vC 4jllC 4jvvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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: 17808.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) |
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#2: Chemical | ChemComp-RB / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.74 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 4.2 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: RbCl 0.1M, Sodium Citrate 0.1M, PEG 1000 40%, microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 2, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 11749 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 40.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ETJ Resolution: 2.411→29.396 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.36 / Phase error: 26.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.62 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.411→29.396 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.9622 Å / Origin y: 1.3494 Å / Origin z: -18.8879 Å
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Refinement TLS group | Selection details: all |