+Open data
-Basic information
Entry | Database: PDB / ID: 2vec | ||||||
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Title | The crystal structure of the protein YhaK from Escherichia coli | ||||||
Components | PIRIN-LIKE PROTEIN YHAK | ||||||
Keywords | CYTOSOLIC PROTEIN / ROS / BICUPIN / SULFENIC ACID / REACTIVE CYSTEINE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Gurmu, D. / Lu, J. / Johnson, K.A. / Nordlund, P. / Holmgren, A. / Erlandsen, H. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: The Crystal Structure of the Protein Yhak from Escherichia Coli Reveals a New Subclass of Redox Sensitive Enterobacterial Bicupins. Authors: Gurmu, D. / Lu, J. / Johnson, K.A. / Nordlund, P. / Holmgren, A. / Erlandsen, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vec.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vec.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vec_validation.pdf.gz | 427.8 KB | Display | wwPDB validaton report |
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Full document | 2vec_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 2vec_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 2vec_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2vec ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2vec | 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
#1: Protein | Mass: 28618.371 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-233 Source method: isolated from a genetically manipulated source Details: CYS122 IS OXIDIZED TO A SULFENIC ACID. AN INTRAMOLECULAR DISULFIDE BOND BETWEEN CYS10 AND CYS204. Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42624 | ||
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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 0.1 M CITRIC ACID, PH 5.0, 2.0 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9797 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 25, 2005 / Details: MIRROR |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→36.42 Å / Num. obs: 23745 / % possible obs: 97.8 % / Observed criterion σ(I): 4 / Redundancy: 19.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.3 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→21.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.13 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→21.75 Å
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