+Open data
-Basic information
Entry | Database: PDB / ID: 8c0h | |||||||||||||||
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Title | Crystal structure of guanidinase from Nitrospira inopinata | |||||||||||||||
Components | Putative agmatinase 2 | |||||||||||||||
Keywords | METAL BINDING PROTEIN / comammox / guanidine / guanidinase / complete ammonia oxidizer | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Candidatus Nitrospira inopinata (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||||||||
Authors | Puehringer, D. | |||||||||||||||
Funding support | Austria, European Union, 4items
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Citation | Journal: To Be Published Title: Growth of complete ammonia oxidizers on guanidine Authors: Palatinszky, M. / Herbold, C.W. / Sedlacek, C.J. / Puehringer, D. / Wasmund, K. / Nielsen, P.H. / Dueholm, M.S. / Jehmlich, N. / Grusek, R. / Kostan, J. / Krasnici, N. / Palmetzhofer, J. / ...Authors: Palatinszky, M. / Herbold, C.W. / Sedlacek, C.J. / Puehringer, D. / Wasmund, K. / Nielsen, P.H. / Dueholm, M.S. / Jehmlich, N. / Grusek, R. / Kostan, J. / Krasnici, N. / Palmetzhofer, J. / Hofmann, T. / Zumstein, M. / Djinovic-Carugo, K. / Daims, H. / Wagner, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c0h.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8c0h.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8c0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c0h_validation.pdf.gz | 11.4 MB | Display | wwPDB validaton report |
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Full document | 8c0h_full_validation.pdf.gz | 11.4 MB | Display | |
Data in XML | 8c0h_validation.xml.gz | 175.2 KB | Display | |
Data in CIF | 8c0h_validation.cif.gz | 255.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/8c0h ftp://data.pdbj.org/pub/pdb/validation_reports/c0/8c0h | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Experimental dataset #1 | Data reference: 10.15151/ESRF-ES-771426868 / Data set type: diffraction image 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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-Components
#1: Protein | Mass: 41716.457 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Nitrospira inopinata (bacteria) Gene: speB, NITINOP_1173 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4KUT0, agmatinase #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-SO4 / #4: 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: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2022 / Details: Vertical CRL / Horizontal Eliptical mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→45.01 Å / Num. obs: 583936 / % possible obs: 92.89 % / Redundancy: 2.3 % / Biso Wilson estimate: 22.07 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1064 / Rpim(I) all: 0.07673 / Rrim(I) all: 0.141 / Net I/σ(I): 4.66 |
Reflection shell | Resolution: 1.58→1.636 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.191 / Mean I/σ(I) obs: 0.56 / Num. unique obs: 53686 / CC1/2: 0.256 / CC star: 0.639 / Rpim(I) all: 0.9081 / Rrim(I) all: 1.506 / % possible all: 85.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→45.01 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→45.01 Å
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LS refinement shell |
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