+Open data
-Basic information
Entry | Database: PDB / ID: 1hqq | ||||||
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Title | MINIPROTEIN MP-2 (M9A) COMPLEX WITH STREPTAVIDIN | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / Conformational Ensemble / mini-proteins / Disulphide constrained loops / Entropically restrained proteins / peptides | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yang, H.W. / Liu, D.Q. / Fan, X. / White, M.A. / Fox, R.O. | ||||||
Citation | Journal: To be Published Title: Conformational Ensemble Analysis of Ligand Binding in Streptavidin Mini-protein Complexes Authors: Yang, H.W. / Liu, D.Q. / Fan, X. / White, M.A. / Fox, R.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hqq.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hqq.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hqq ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hqq | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 13409.466 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Protein/peptide | Mass: 1593.852 Da / Num. of mol.: 4 / Mutation: M9A / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #3: Water | ChemComp-HOH / | |
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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: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 100 mM potassium acetate, ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 20, 2000 / Details: Multilayer |
Radiation | Monochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20.84 Å / Num. all: 63318 / Num. obs: 163318 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.46 % / Biso Wilson estimate: 12.5 Å2 / Limit h max: 34 / Limit h min: -34 / Limit k max: 52 / Limit k min: -34 / Limit l max: 33 / Limit l min: 0 / Observed criterion F max: 569614.15 / Observed criterion F min: 0.316 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2754 / Rsym value: 0.302 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Mp-2 streptavidin complex Resolution: 1.7→20.84 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high rms absF: 569571.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 38.6719 Å2 / ksol: 0.351859 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.9 Å2 / Biso mean: 17.08 Å2 / Biso min: 3.77 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20.84 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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