+Open data
-Basic information
Entry | Database: PDB / ID: 5k95 | ||||||
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Title | Crystal Structure of GTP Cyclohydrolase-IB with 8-oxo-GTP | ||||||
Components | GTP cyclohydrolase FolE2 | ||||||
Keywords | HYDROLASE / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Alvarez, J. / Stec, B. / Swairjo, M.A. | ||||||
Citation | Journal: Biochem.J. / Year: 2017 Title: Mechanism and catalytic strategy of the prokaryotic-specific GTP cyclohydrolase-IB. Authors: Paranagama, N. / Bonnett, S.A. / Alvarez, J. / Luthra, A. / Stec, B. / Gustafson, A. / Iwata-Reuyl, D. / Swairjo, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k95.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k95.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k95_validation.pdf.gz | 735.2 KB | Display | wwPDB validaton report |
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Full document | 5k95_full_validation.pdf.gz | 749.3 KB | Display | |
Data in XML | 5k95_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 5k95_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/5k95 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/5k95 | HTTPS FTP |
-Related structure data
Related structure data | 5k9gC 3d1t C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 28811.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria) Strain: ATCC 700825 / FA 1090 / Gene: folE2, NGO0387 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F9K6, GTP cyclohydrolase I #2: Chemical | ChemComp-8GT / | #3: Chemical | ChemComp-ZN / | #4: 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: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 10-16% polyethylene glycol 6000, 0.6-1.4 M LiCl, 60 mM HEPES pH 8.2, 40 mM HEPES |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→46.07 Å / Num. obs: 13898 / % possible obs: 99.7 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.833 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D1T 3d1t Resolution: 2.77→46.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.34 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.584 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→46.07 Å
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