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Yorodumi- PDB-3kre: Crystal structure of phosphoribosylaminoimidazole-succinocarboxam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kre | ||||||
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Title | Crystal structure of phosphoribosylaminoimidazole-succinocarboxamide synthase from Ehrlichia chaffeensis at 1.8A resolution | ||||||
Components | Phosphoribosylaminoimidazole-succinocarboxamide synthase | ||||||
Keywords | LIGASE / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / EHRLICHIA CHAFFEENSIS / PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE / ATP-binding / Nucleotide-binding / Purine biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Ehrlichia chaffeensis str. Arkansas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of phosphoribosylaminoimidazole-succinocarboxamide synthase from Ehrlichia chaffeensis at 1.8A resolution Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Edwards, T.E. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kre.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kre.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/3kre ftp://data.pdbj.org/pub/pdb/validation_reports/kr/3kre | HTTPS FTP |
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-Related structure data
Related structure data | 2ywvS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30365.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ehrlichia chaffeensis str. Arkansas (bacteria) Strain: ARKANSAS / Gene: purC, ECH_0290 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2GHH2, phosphoribosylaminoimidazolesuccinocarboxamide synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: 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: 2.33 Å3/Da / Density % sol: 47.26 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: EBS SCREEN JCSG+ G1: 100MM HEPES PH 7.0, 30% JEFFAMINE ED-2001; EHCHA.00530.A AT 50MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 9, 2009 / Details: Rigaku VariMax HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 26063 / Num. obs: 24514 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.61 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.59 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1557 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2ywv modified with CCP4 program CHAINSAW Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.559 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 17.367 Å / Origin y: 0.572 Å / Origin z: 11.195 Å
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Refinement TLS group |
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