+Open data
-Basic information
Entry | Database: PDB / ID: 3d54 | ||||||
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Title | Structure of PurLQS from Thermotoga maritima | ||||||
Components |
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Keywords | LIGASE / alpha-beta structure / ATP-binding / Nucleotide-binding / Purine biosynthesis / Glutamine amidotransferase / LIGASE-UNKNOWN FUNCTION COMPLEX | ||||||
Function / homology | Function and homology information phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / glutaminase / glutaminase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / glutamine metabolic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Ealick, S.E. / Morar, M. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation. Authors: Morar, M. / Hoskins, A.A. / Stubbe, J. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d54.cif.gz | 549.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d54.ent.gz | 455.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/3d54 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/3d54 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 69108.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: purL / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0X3, phosphoribosylformylglycinamidine synthase #2: Protein | Mass: 9656.207 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0X1, phosphoribosylformylglycinamidine synthase #3: Protein | Mass: 23746.238 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: purQ / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0X2, phosphoribosylformylglycinamidine synthase #4: Chemical | #5: Chemical | |
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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: 5.62 Å3/Da / Density % sol: 78.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 55% MPD, 0.1M HEPES, 7% xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→45.7 Å / Num. all: 93673 / Num. obs: 78498 / % possible obs: 83.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.5→3.72 Å / % possible all: 66.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→45.7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 127056.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: BULK SOLVENT MODEL USED. THE IDENTITY OF THE METAL ION PRESENT IN THE TMPURLQS STRUCTURE IS UNCERTAIN
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.21 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→45.7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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