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Yorodumi- PDB-6ypx: Human histidine triad nucleotide-binding protein 2 (hHINT2) refin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ypx | |||||||||
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Title | Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 2.11 A in C2221 space group | |||||||||
Components | Histidine triad nucleotide-binding protein 2, mitochondrial | |||||||||
Keywords | HYDROLASE / Nucleotide binding protein | |||||||||
Function / homology | Function and homology information negative regulation of peptidyl-lysine acetylation / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / nucleotide binding / apoptotic process ...negative regulation of peptidyl-lysine acetylation / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / nucleotide binding / apoptotic process / mitochondrion / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | |||||||||
Authors | Dolot, R.D. / Wlodarczyk, A. / Bujacz, G.D. / Nawrot, B.C. | |||||||||
Funding support | Poland, 1items
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Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2021 Title: Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A. Authors: Dolot, R. / Krakowiak, A. / Kaczmarek, R. / Wlodarczyk, A. / Pichlak, M. / Nawrot, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ypx.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ypx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ypx_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6ypx_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 6ypx_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 6ypx_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypx ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypx | HTTPS FTP |
-Related structure data
Related structure data | 6yi0C 6yprC 6yqdC 6yqmC 6yvpC 3tw2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 17183.725 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HINT2 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BX68, Hydrolases #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 3.99 Å3/Da / Density % sol: 69.15 % / Description: rectangular plates |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium citrate, 0.1 M sodium cacodylate, 30 % 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9669 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9669 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→102.94 Å / Num. obs: 46164 / % possible obs: 99.6 % / Redundancy: 12.2 % / Biso Wilson estimate: 15.482 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.094 / Rrim(I) all: 0.24 / Χ2: 1 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.11→2.17 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 2 / Num. unique obs: 3623 / CC1/2: 0.697 / Rpim(I) all: 0.568 / Rrim(I) all: 1.194 / Χ2: 0.96 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TW2 Resolution: 2.11→102.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.712 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.345 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→102.94 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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