+Open data
-Basic information
Entry | Database: PDB / ID: 2j4r | ||||||
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Title | Structural Study of the Aquifex aeolicus PPX-GPPA enzyme | ||||||
Components | EXOPOLYPHOSPHATASE | ||||||
Keywords | HYDROLASE / PPGPP / AQUIFEX AEOLICUS / STRINGENT RESPONSE / EXOPOLYPHOSPHATASE / GUANOSINE PENTAPHOSPHATE | ||||||
Function / homology | Function and homology information guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity / pyrophosphatase activity / nucleobase-containing small molecule interconversion / regulation of transcription by RNA polymerase II / metal ion binding Similarity search - Function | ||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Kristensen, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of the Ppx/Gppa Phosphatase from Aquifex Aeolicus in Complex with the Alarmone Ppgpp Authors: Kristensen, O. / Ross, B. / Gajhede, M. #1: Journal: Biochemistry / Year: 2004 Title: Structural Characterization of the Stringent Response Related Exopolyphosphatase-Guanosine Pentaphosphate Phosphohydrolase Protein Family Authors: Kristensen, O. / Laurberg, M. / Liljas, A. / Kastrup, J.S. / Gajhede, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j4r.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j4r.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 2j4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j4r_validation.pdf.gz | 864 KB | Display | wwPDB validaton report |
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Full document | 2j4r_full_validation.pdf.gz | 902.3 KB | Display | |
Data in XML | 2j4r_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 2j4r_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j4r ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j4r | HTTPS FTP |
-Related structure data
Related structure data | 1t6cS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.98603, 0.01721, 0.16569), Vector: |
-Components
#1: Protein | Mass: 34998.434 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-310 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Plasmid: PET28-A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O67040 #2: Chemical | ChemComp-G4P / | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.36 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | Details: SODIUM ACETATE, MES, MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.085 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.085 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→74.54 Å / Num. obs: 85915 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.71→2.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T6C Resolution: 2.71→61.02 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1874853.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.7665 Å2 / ksol: 0.328112 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.71→61.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.88 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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