+Open data
-Basic information
Entry | Database: PDB / ID: 1zcp | ||||||
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Title | Crystal Structure of a catalytic site mutant E. coli TrxA (CACA) | ||||||
Components | Thioredoxin 1 | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Collet, J.-F. / Peisach, D. / Bardwell, J.C. / Xu, Z. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: The crystal structure of TrxA(CACA): Insights into the formation of a [2Fe-2S] iron-sulfur cluster in an Escherichia coli thioredoxin mutant Authors: Collet, J.-F. / Peisach, D. / Bardwell, J.C. / Xu, Z. #1: Journal: Science / Year: 2004 Title: An engineered pathway for the formation of protein disulfide bonds Authors: Masip, L. / Pan, J.L. / Haldar, S. / Penner-Hahn, J.E. / DeLisa, M.P. / Georgiou, G. / Bardwell, J.C.A. / Collet, J.-F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zcp.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zcp.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/1zcp ftp://data.pdbj.org/pub/pdb/validation_reports/zc/1zcp | HTTPS FTP |
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-Related structure data
Related structure data | 1xobS 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: 11675.376 Da / Num. of mol.: 4 / Mutation: G33A, P34C, C35A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, fipA, tsnC / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25 #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: 2.16 Å3/Da / Density % sol: 43.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG4000, 0.1 M Tris, 0.2 M Magnesium chloride, 4% acetonitrile, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0023 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0023 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.41 Å / Num. all: 18001 / Num. obs: 15211 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.5 Å2 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XOB Resolution: 2.3→43.41 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 369499.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.8401 Å2 / ksol: 0.322577 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→43.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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