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Yorodumi- PDB-6rqu: X-ray crystal structure of H/D exchanged (H/D) small monoclinic u... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rqu | ||||||
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Title | X-ray crystal structure of H/D exchanged (H/D) small monoclinic unit cell CA IX SV. | ||||||
Components | Carbonic anhydrase 9 | ||||||
Keywords | PROTON TRANSPORT / carbonic anhydrase / CA IX / surface variant | ||||||
Function / homology | Function and homology information Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.393 Å | ||||||
Authors | Fisher, Z. / Koruza, K. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX. Authors: Koruza, K. / Lafumat, B. / Nyblom, M. / Mahon, B.P. / Knecht, W. / McKenna, R. / Fisher, S.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rqu.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rqu.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rqu_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 6rqu_full_validation.pdf.gz | 444.2 KB | Display | |
Data in XML | 6rqu_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 6rqu_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/6rqu ftp://data.pdbj.org/pub/pdb/validation_reports/rq/6rqu | HTTPS FTP |
-Related structure data
Related structure data | 6rqnC 6rqqC 6rqwC 5dvxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28092.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16790, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% (w/v) PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→40 Å / Num. obs: 48352 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.39→1.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2406 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dvx Resolution: 1.393→32.69 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.4 Å2 / Biso mean: 29.7701 Å2 / Biso min: 15.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.393→32.69 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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