+Open data
-Basic information
Entry | Database: PDB / ID: 1zzy | ||||||
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Title | Crystal Structure of Thioredoxin Mutant L7V | ||||||
Components | Thioredoxin 1 | ||||||
Keywords | ELECTRON TRANSPORT / Alpha/Beta | ||||||
Function / homology | Function and homology information positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / oxidoreductase activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Thioredoxin Mutant L7V Authors: Gavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zzy.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zzy.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zzy_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 1zzy_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 1zzy_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1zzy_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/1zzy ftp://data.pdbj.org/pub/pdb/validation_reports/zz/1zzy | HTTPS FTP |
-Related structure data
Related structure data | 2trxS 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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Unit cell |
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-Components
#1: Protein | Mass: 11673.360 Da / Num. of mol.: 2 / Mutation: L7V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, fipA, tsnC / Plasmid: pTk100 / Production host: Escherichia coli (E. coli) / Strain (production host): JF521 / References: UniProt: P00274, UniProt: P0AA25*PLUS #2: 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: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 295 K / Method: counter-diffusion / pH: 3.8 Details: 10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jan 7, 2005 / Details: Montel Optics |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40.26 Å / Num. all: 5671 / Num. obs: 5671 / % possible obs: 88.7 % / Redundancy: 1.46 % / Biso Wilson estimate: 12.8 Å2 / Limit h max: 13 / Limit h min: -12 / Limit k max: 14 / Limit k min: -12 / Limit l max: 17 / Limit l min: 0 / Observed criterion F max: 1312437.97 / Observed criterion F min: 3.46 / Rsym value: 0.1236 / Net I/σ(I): 6.57 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.38 % / Mean I/σ(I) obs: 2.82 / Num. unique all: 605 / Rsym value: 0.374 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A:2trx.pdb Resolution: 2.5→38.69 Å / Rfactor Rfree error: 0.016 / Occupancy max: 1 / Occupancy min: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: XTALVIEW and MOLBROBITY were also used for the refinement.
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 50.8937 Å2 / ksol: 0.324627 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.55 Å2 / Biso mean: 23.29 Å2 / Biso min: 1.01 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→38.69 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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