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Yorodumi- PDB-5ku6: Crystal structure for the complex of human carbonic anhydrase IV ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ku6 | |||||||||
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Title | Crystal structure for the complex of human carbonic anhydrase IV and methazolamide | |||||||||
Components | Carbonic anhydrase 4 | |||||||||
Keywords | lyase/lyase inhibitor / Carbonic anhydrase / Intrinsic thermodynamics / lyase / inhibitor / lyase-lyase inhibitor complex | |||||||||
Function / homology | Function and homology information bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network ...bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / apical plasma membrane / external side of plasma membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular exosome / zinc ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Chen, Z. / Waheed, A. / Di Cera, E. / Sly, W.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Eur. Biophys. J. / Year: 2018 Title: Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV. Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / ...Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / Revuckiene, J. / Manakova, E. / Grazulis, S. / Matuliene, J. / Di Cera, E. / Sly, W.S. / Matulis, D. #1: Journal: PNAS / Year: 1996 Title: Crystal structure of the secretory form of membrane-associated human carbonic anhydrase IV at 2.8 A resolution Authors: Stams, T. / Nair, S.K. / Okuyama, T. / Waheed, A. / Sly, W.S. / Christianson, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ku6.cif.gz | 468.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ku6.ent.gz | 387.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ku6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ku6_validation.pdf.gz | 503.1 KB | Display | wwPDB validaton report |
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Full document | 5ku6_full_validation.pdf.gz | 515.9 KB | Display | |
Data in XML | 5ku6_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 5ku6_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/5ku6 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5ku6 | HTTPS FTP |
-Related structure data
Related structure data | 5ipzC 5jn8C 5jn9C 5jnaC 5jncC 1zncS 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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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 30364.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22748, carbonic anhydrase |
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-Non-polymers , 6 types, 939 molecules
#2: Chemical | ChemComp-MZM / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has protein modification | 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: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Na acetate, 200 mM AmSO4 and 23% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2015 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 110310 / % possible obs: 97.3 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.1 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZNC Resolution: 1.8→95.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.494 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.503 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→95.78 Å
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Refine LS restraints |
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