+Open data
-Basic information
Entry | Database: PDB / ID: 1z3x | ||||||
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Title | Structure of Gun4 from Thermosynechococcus elongatus | ||||||
Components | putative cytidylyltransferase | ||||||
Keywords | Transferase Activator | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Davison, P.A. / Schubert, H.L. / Reid, J.D. / Iorg, C.D. / Robinson, H. / Hill, C.P. / Hunter, C.N. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural and Biochemical Characterization of Gun4 Suggests a Mechanism for Its Role in Chlorophyll Biosynthesis(,). Authors: Davison, P.A. / Schubert, H.L. / Reid, J.D. / Iorg, C.D. / Heroux, A. / Hill, C.P. / Hunter, C.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z3x.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z3x.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 1z3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z3x_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
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Full document | 1z3x_full_validation.pdf.gz | 421.2 KB | Display | |
Data in XML | 1z3x_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1z3x_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/1z3x ftp://data.pdbj.org/pub/pdb/validation_reports/z3/1z3x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27465.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Gene: Gun4 / Plasmid: GST-4-TI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+ / References: UniProt: Q8DIJ1 |
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#2: 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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2 M NH3Cl, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 0.976, 0.9802, 0.9660 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 42484 / Num. obs: 42482 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.068 | ||||||||||||
Reflection shell | Resolution: 1.5→1.539 Å / Rmerge(I) obs: 0.467 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.315 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.161 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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