+Open data
-Basic information
Entry | Database: PDB / ID: 3hz4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Thioredoxin from Methanosarcina mazei | ||||||
Components | Thioredoxin | ||||||
Keywords | OXIDOREDUCTASE / NYSGXRC / PSI-II / reduced form / thioredoxin / 11215h / Protein structure Initiative / structural genomics / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thioredoxin Function and homology information | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Thioredoxin from Methanosarcina mazei Authors: Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hz4.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hz4.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hz4 ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hz4 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16258.526 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: MM_2079 / Plasmid: TOP10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8PV92 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.17 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% Peg 3350, 0.1M Bis Tris pH 5.5, 0.2M LiSo4, 0.1M EDTA, 20% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9797 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2009 / Details: Mirrors |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection twin | Type: hemihedral / Operator: -h,-k,l / Fraction: 0.38 |
Reflection | Resolution: 2.3→50 Å / Num. all: 18041 / Num. obs: 18041 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.5 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 21 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 9.6 / Num. unique all: 1639 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.592 / SU ML: 0.139 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The data is hemihedral twinning with twinning operator (-h, -k, l) and corresponding twinned fraction: 0.38.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.48 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.257→2.3 Å / Total num. of bins used: 20
|