+Open data
-Basic information
Entry | Database: PDB / ID: 5k9g | |||||||||
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Title | Crystal Structure of GTP Cyclohydrolase-IB with Tris | |||||||||
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: 1.9 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. #1: Journal: J.Bacteriol. / Year: 2009 Title: Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. Authors: Sankaran, B. / Bonnett, S.A. / Shah, K. / Gabriel, S. / Reddy, R. / Schimmel, P. / Rodionov, D.A. / de Crecy-Lagard, V. / Helmann, J.D. / 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 | 5k9g.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k9g.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 5k9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k9g_validation.pdf.gz | 470.2 KB | Display | wwPDB validaton report |
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Full document | 5k9g_full_validation.pdf.gz | 475.3 KB | Display | |
Data in XML | 5k9g_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 5k9g_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/5k9g ftp://data.pdbj.org/pub/pdb/validation_reports/k9/5k9g | HTTPS FTP |
-Related structure data
Related structure data | 5k95C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 395 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-FMT / | #6: 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: 2.3 Å3/Da / Density % sol: 46.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: (PEG 6000, 10-16%), LiCl (1-1.4 M), Tris (50 mM, pH 9.0) and Tris-Cl (50 mM, pH 7.0). Enzym sample prepared at 10 mg/mL in 50 mM Tris-HCl, 50 mM KCl, 1 mM DTT, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9767 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→68.16 Å / Num. obs: 41832 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 36.17 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.05 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D1T 3d1t Resolution: 1.9→68.16 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.63 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 42.031 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→68.16 Å
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Refine LS restraints |
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