+Open data
-Basic information
Entry | Database: PDB / ID: 1byz | |||||||||
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Title | DESIGNED PEPTIDE ALPHA-1, P1 FORM | |||||||||
Components | PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1") | |||||||||
Keywords | DE NOVO PROTEIN / HELICAL BILAYER / BIOMATERIAL | |||||||||
Function / homology | ETHANOLAMINE Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.9 Å | |||||||||
Authors | Prive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D. | |||||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle. Authors: Prive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D. #1: Journal: Protein Sci. / Year: 1999 Title: Centrosymmetric Bilayers in the 0.75A Resolution Structure of a Designed Alpha- Helical Peptide, D, L-Alpha-1 Authors: Patterson, W.R. / Anderson, D.H. / Degrado, W.F. / Cascio, D. / Eisenberg, D. #2: Journal: Science / Year: 1990 Title: Crystal Structure of Alpha-1: Implications for Protein Design Authors: Hill, C.P. / Anderson, D.H. / Wesson, L. / Degrado, W.F. / Eisenberg, D. #3: Journal: Proteins / Year: 1986 Title: The Design, Synthesis, and Crystallization of an Alpha-Helical Peptide Authors: Eisenberg, D. / Wilcox, W. / Eshita, S.M. / Pryciak, P.M. / Ho, S.P. / De Grado, W.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1byz.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1byz.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1byz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1byz_validation.pdf.gz | 410.7 KB | Display | wwPDB validaton report |
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Full document | 1byz_full_validation.pdf.gz | 410.6 KB | Display | |
Data in XML | 1byz_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1byz_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1byz ftp://data.pdbj.org/pub/pdb/validation_reports/by/1byz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide , 1 types, 4 molecules ABCD
#1: Protein/peptide | Mass: 1441.775 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: N TERMINI ARE ACETYLATED / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 37 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-MRD / ( | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | MPD 513 IS BUILT IN TWO OVERLAPPIN |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.13 % / Description: SNB SUCCESS RATE WAS 5%. | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 Details: 91% 2-METHYL-2,4-PENTANEDIOL, 78mM TRIETHANOLAMINE-HCL pH8, 52mM ETHANOLAMINE-HCL pH9.75, pH 8.0, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of peptide and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1994 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→25.7 Å / Num. obs: 23681 / % possible obs: 85.9 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 0.076 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 0.9→0.93 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.141 / % possible all: 36 |
Reflection | *PLUS Highest resolution: 0.9 Å / Lowest resolution: 25.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 36 % / Num. unique obs: 1011 / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 4.3 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS Starting model: 448 RANDOM ATOMS Resolution: 0.9→25.7 Å / Num. parameters: 4695 / Num. restraintsaints: 5898 / Cross valid method: FREE R / σ(F): 2 StereochEM target val spec case: ETHANOLAMINE AND MPD RESTRAINTS WERE DERIVED BY ANALOGY TO OTHER SIMILAR GROUPS Stereochemistry target values: ENGH AND HUBER Details: MORE LOW-OCCUPANCY DISCRETE DISORDER COULD BE BUILT FOR SOLVENT AND PEPTIDE, BUT WOULD EXCESSIVELY INCREASE THE NUMBER OF REFINEABLE PARAMETERS.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 544 / Occupancy sum non hydrogen: 478.97 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→25.7 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 93 and 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 0.9 Å / Rfactor obs: 0.086 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 0.9 Å / Lowest resolution: 1.01 Å / Rfactor Rwork: 0.164 |