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Yorodumi- PDB-7zhf: GPN-loop GTPase from Sulfolobus acidocaldarius closed state (GppNHp) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zhf | ||||||
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Title | GPN-loop GTPase from Sulfolobus acidocaldarius closed state (GppNHp) | ||||||
Components | GTPase | ||||||
Keywords | UNKNOWN FUNCTION / GPN-loop / self-activating / GTPase / homodimer | ||||||
Function / homology | GPN-loop GTPase / Conserved hypothetical ATP binding protein / hydrolase activity / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Korf, L. / Essen, L.-O. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Mbio / Year: 2023 Title: Archaeal GPN-loop GTPases involve a lock-switch-rock mechanism for GTP hydrolysis. Authors: Korf, L. / Ye, X. / Vogt, M.S. / Steinchen, W. / Watad, M. / van der Does, C. / Tourte, M. / Sivabalasarma, S. / Albers, S.-V. / Essen, L.-O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zhf.cif.gz | 203.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zhf.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 7zhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zhf_validation.pdf.gz | 802.7 KB | Display | wwPDB validaton report |
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Full document | 7zhf_full_validation.pdf.gz | 808.5 KB | Display | |
Data in XML | 7zhf_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7zhf_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/7zhf ftp://data.pdbj.org/pub/pdb/validation_reports/zh/7zhf | HTTPS FTP |
-Related structure data
Related structure data | 7zhkC 1yr7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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, 1 molecules A
#1: Protein | Mass: 30859.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Gene: ATY89_00095, ATZ20_03140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U2WWJ1 |
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-Non-polymers , 5 types, 197 molecules
#2: Chemical | ChemComp-GNP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.018 M CaCl2, 0.09M Sodium acetate pH=4.6, 27% (v/v) MPD, 10% (v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2020 / Details: flexible two-stage focusing X-ray optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.09 Å / Num. obs: 24163 / % possible obs: 90.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.027 / Rrim(I) all: 0.038 / Χ2: 0.71 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 24086 / CC1/2: 0.92 / Rpim(I) all: 0.385 / Rrim(I) all: 0.573 / Χ2: 1.07 / % possible all: 54.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YR7 Resolution: 1.8→41.09 Å / SU ML: 0.1564 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3241 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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