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Yorodumi- PDB-3kcq: Crystal structure of phosphoribosylglycinamide formyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kcq | ||||||
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Title | Crystal structure of phosphoribosylglycinamide formyltransferase from anaplasma phagocytophilum | ||||||
Components | Phosphoribosylglycinamide formyltransferase | ||||||
Keywords | TRANSFERASE / structural genomics / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process Similarity search - Function | ||||||
Biological species | Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of phosphoribosylglycinamide formyltransferase from anaplasma phagocytophilum Authors: Staker, B.L. / Edwards, T. / Dieterich, M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kcq.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kcq.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/3kcq ftp://data.pdbj.org/pub/pdb/validation_reports/kc/3kcq | HTTPS FTP |
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-Related structure data
Related structure data | 1zlyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23518.158 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis) Strain: HZ / Gene: purN, APH_0230 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2GLA4, phosphoribosylglycinamide formyltransferase 1 #2: Chemical | ChemComp-GOL / #3: 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: 2.87 Å3/Da / Density % sol: 57.09 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5 Details: EMERALD JCSG SCREEN CONDITION A2. 100 MM CITRATE PH 5.0, 20% PEG 3000. PROTEIN CONCENTRATION 54 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97953 / Wavelength: 0.97953 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Sep 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 45778 / % possible obs: 85.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.449 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZLY Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.856 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.25 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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