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Yorodumi- PDB-2hyz: Crystal structure of an 8 repeat consensus TPR superhelix (orthor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hyz | ||||||
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Title | Crystal structure of an 8 repeat consensus TPR superhelix (orthorombic crystal form) | ||||||
Components | SYNTHETIC CONSENSUS TPR PROTEIN | ||||||
Keywords | DE NOVO PROTEIN / TPR / tetratricopeptide / protein design / protein stability / superhelix | ||||||
Function / homology | Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / SAMARIUM (III) ION Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.3 Å | ||||||
Authors | Kajander, T. / Cortajarena, A.L. / Regan, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins. Authors: Kajander, T. / Cortajarena, A.L. / Mochrie, S. / Regan, L. #1: Journal: J.Am.Chem.Soc. / Year: 2005 Title: A new folding paradigm for repeat proteins. Authors: Kajander, T. / Cortajarena, A.L. / Main, E. / Mochrie, S. / Regan, L. | ||||||
History |
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Remark 400 | COMPOUND THE COMPLETE CRYSTALLIZED SEQUENCE IS TWICE LONGER THAN THE SUBMITTED ONE. THE LINK RECORD ...COMPOUND THE COMPLETE CRYSTALLIZED SEQUENCE IS TWICE LONGER THAN THE SUBMITTED ONE. THE LINK RECORD IS PROVIDED TO CONNECT THE DEPOSITED PART OF THE SEQUENCE WITH THE SECOND PART OF THE COMPLETE CRYSTALLIZED 8-REPEAT MOLECULE THAT CAN BE GENERATED FROM THE DEPOSITED COORDINATES USING THE MATRIX PROVIDED IN REMARK 350. | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE MOLECULE REPRESENTS A PSEUDO-INFINITE FIBER. THE SECOND PART OF THE COMPLETE COVALENT MOLECULE CAN BE GENERATED BY APPLYING THE MATRIX PROVIDED IN REMARK 350. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hyz.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hyz.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/2hyz ftp://data.pdbj.org/pub/pdb/validation_reports/hy/2hyz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains one half of the whole covalent protein molecule (4 TPR repeats), the other half is generated by crystallographic symmetry. |
-Components
#1: Protein | Mass: 16151.237 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE SEQUENCE OF THE PROTEIN WAS DESIGNED AND THEN EXPRESSED IN E.COLI BL21(DE3), PLASMID pPRO-XHTA | ||
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#2: Chemical | #3: 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: 54.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5 Details: 100 mM Acetate, 25% MPD, 50 mM SmCl3, pH 5.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.4 % / Av σ(I) over netI: 9.2 / Number: 51310 / Rmerge(I) obs: 0.101 / Χ2: 1.61 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 14975 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.3→50 Å / Num. all: 14975 / Num. obs: 14975 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.101 / Χ2: 1.609 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.75 / FOM acentric: 0.76 / FOM centric: 0.68 / Reflection: 6196 / Reflection acentric: 5113 / Reflection centric: 1083 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.224 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.241 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.527 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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