+Open data
-Basic information
Entry | Database: PDB / ID: 1zsz | ||||||
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Title | Crystal structure of a computationally designed SspB heterodimer | ||||||
Components | (Stringent starvation protein B homolog) x 3 | ||||||
Keywords | DE NOVO PROTEIN / protein design / AAA / adaptor / specificity | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bolon, D.N. / Grant, R.A. / Baker, T.A. / Sauer, R.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Specificity versus stability in computational protein design. Authors: Bolon, D.N. / Grant, R.A. / Baker, T.A. / Sauer, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zsz.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zsz.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/1zsz ftp://data.pdbj.org/pub/pdb/validation_reports/zs/1zsz | HTTPS FTP |
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-Related structure data
Related structure data | 1ou9S 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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2 |
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3 |
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Unit cell |
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Details | chain b and c compose one biological unit, while chain A, forms a dimer across a crystal axis (to a crystallographically related chain A) |
-Components
#1: Protein | Mass: 12511.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: sspB / Plasmid: pET21, pACYCDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P45206 | ||
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#2: Protein | Mass: 12578.135 Da / Num. of mol.: 1 / Mutation: A15S,Y16L,V101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: sspB / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P45206 | ||
#3: Protein | Mass: 14769.420 Da / Num. of mol.: 1 / Mutation: L12Y,A15G,Y16F,V101M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: sspB / Plasmid: pACYCDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P45206 | ||
#4: Chemical | #5: 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: 2.68 Å3/Da / Density % sol: 54.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG 6000, CaCl2, sodium cacodylate, KCl, glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2004 |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 28612 / Num. obs: 28612 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.371 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ou9 chain A Resolution: 2→29.15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 432252.67 / Data cutoff high rms absF: 432252.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Chain A forms a dimer across a crystal axis and is an average of chains B and C. During refinement, residues which are different in chains B and C, were modeled with truncated side chains in ...Details: Chain A forms a dimer across a crystal axis and is an average of chains B and C. During refinement, residues which are different in chains B and C, were modeled with truncated side chains in chain A. The side chains for these residues are present in the chains B and C. The B/C dimer shows the asymmetric packing at the dimer interface that was introduced by computational design and was the focus of this study.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.2607 Å2 / ksol: 0.352752 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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