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Yorodumi- PDB-4zsz: Structure of a fusion protein with a helix linker, 2ARH-3-3KAW-3.0 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zsz | ||||||
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Title | Structure of a fusion protein with a helix linker, 2ARH-3-3KAW-3.0 | ||||||
Components | Uncharacterized Fusion Protein | ||||||
Keywords | UNKNOWN FUNCTION / protein design / bionanotechnology / protein assembly / symmetry / biomaterials | ||||||
Function / homology | Uncharacterised conserved protein UCP017998 / Protein of unknown function (DUF1122) / Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / Acyl-CoA N-acyltransferase / DUF1122 domain-containing protein / Four-helix bundle copper-binding protein Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.251 Å | ||||||
Authors | Lai, Y.-T. / Yeates, T.O. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2015 Title: On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker. Authors: Lai, Y.T. / Jiang, L. / Chen, W. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zsz.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zsz.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zsz_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 4zsz_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 4zsz_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4zsz_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/4zsz ftp://data.pdbj.org/pub/pdb/validation_reports/zs/4zsz | HTTPS FTP |
-Related structure data
Related structure data | 4zsvC 4zsxC 2arhS 3kawS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 295 / Label seq-ID: 2 - 295
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-Components
#1: Protein | Mass: 34339.402 Da / Num. of mol.: 2 Mutation: Y138F, E158A, K162A, E166A, Q208H, A209H, R212H, E124A, R293H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria), (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: VF5, ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: aq_1966, PA2107 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67778, UniProt: Q9I208 |
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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: 4.02 Å3/Da / Density % sol: 69.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris (pH=5.5) and 1.5M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 16, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.25→81.927 Å / Num. obs: 8061 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.38 % / Biso Wilson estimate: 163.84 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.128 / Χ2: 0.903 / Net I/σ(I): 12.66 / Num. measured all: 43354 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ARH, 3KAW Resolution: 4.251→46.492 Å / SU ML: 0.76 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.2 / 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 max: 50 Å2 / Biso mean: 49.2866 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.251→46.492 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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