+Open data
-Basic information
Entry | Database: PDB / ID: 5cdx | ||||||
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Title | Crystal structure of conserpin | ||||||
Components | Conserpin | ||||||
Keywords | hydrolase inhibitor / Serine Protease Inhibitor / Aggregation Resistant / Consensus Design / Stability | ||||||
Function / homology | Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Porebski, B.T. / Borg, N.A. / McGowan, S. / Buckle, A.M. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Smoothing a rugged protein folding landscape by sequence-based redesign. Authors: Porebski, B.T. / Keleher, S. / Hollins, J.J. / Nickson, A.A. / Marijanovic, E.M. / Borg, N.A. / Costa, M.G. / Pearce, M.A. / Dai, W. / Zhu, L. / Irving, J.A. / Hoke, D.E. / Kass, I. / ...Authors: Porebski, B.T. / Keleher, S. / Hollins, J.J. / Nickson, A.A. / Marijanovic, E.M. / Borg, N.A. / Costa, M.G. / Pearce, M.A. / Dai, W. / Zhu, L. / Irving, J.A. / Hoke, D.E. / Kass, I. / Whisstock, J.C. / Bottomley, S.P. / Webb, G.I. / McGowan, S. / Buckle, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cdx.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cdx.ent.gz | 115.5 KB | Display | PDB format |
PDBx/mmJSON format | 5cdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cdx_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 5cdx_full_validation.pdf.gz | 424 KB | Display | |
Data in XML | 5cdx_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5cdx_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/5cdx ftp://data.pdbj.org/pub/pdb/validation_reports/cd/5cdx | HTTPS FTP |
-Related structure data
Related structure data | 5cdzC 5ce0C 3ne4S 5ce2 C: citing same article (ref.) S: Starting model for refinement |
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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: 42578.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.24 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystals appeared within 5 days in 0.2 M magnesium chloride hexahydrate, 16% PEG-3350, 10 mM bis-tris, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010 |
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.06 Å / Num. all: 30073 / Num. obs: 15325 / % possible obs: 97.77 % / Redundancy: 2 % / Rmerge(I) obs: 0.04451 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.16 / Num. unique all: 1498 / % possible all: 97.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NE4 Resolution: 2.4→42.06 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.917 Å2 / ksol: 0.315 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→42.06 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: 36.2747 Å / Origin y: 44.5292 Å / Origin z: 57.1267 Å
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Refinement TLS group | Selection details: all |