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Yorodumi- PDB-8slb: X-ray structure of CorA N-terminal domain in complex with conform... -
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-Basic information
Entry | Database: PDB / ID: 8slb | ||||||
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Title | X-ray structure of CorA N-terminal domain in complex with conformation-specific synthetic antibody C12 | ||||||
Components |
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Keywords | METAL TRANSPORT / ion channel / magnesium channel / regulatory domain / divalent metal cation binding protein / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information magnesium ion transmembrane transport / cobalt ion transport / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / protein homooligomerization / magnesium ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Dominik, P.K. / Erramilli, S.K. / Reddy, B.G. / Kossiakoff, A.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2023 Title: Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA. Authors: Erramilli, S.K. / Dominik, P.K. / Deneka, D. / Tokarz, P. / Kim, S.S. / Reddy, B.G. / Skrobek, B.M. / Dalmas, O. / Perozo, E. / Kossiakoff, A.A. #1: Journal: Biorxiv / Year: 2023 Title: Conformation-specific synthetic antibodies discriminate multiple functional states of the ion channel CorA. Authors: Erramilli, S.K. / Dominik, P.K. / Deneka, D. / Tokarz, P. / Kim, S.S. / Reddy, B.G. / Skrobek, B.M. / Dalmas, O. / Perozo, E. / Kossiakoff, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8slb.cif.gz | 295.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8slb.ent.gz | 240 KB | Display | PDB format |
PDBx/mmJSON format | 8slb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/8slb ftp://data.pdbj.org/pub/pdb/validation_reports/sl/8slb | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34277.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: corA, TM_0561 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9WZ31 | ||||
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#2: Antibody | Mass: 25984.107 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) | ||||
#3: Antibody | Mass: 23437.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 8% dextrane sulfate, 17% PEG 3350, 0.02 M citric acid/0.08 M bis-Tris propane pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 15, 2015 / Details: 3.3 Undulator (Undulator A) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.038→45.82 Å / Num. obs: 55678 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.054 / Rrim(I) all: 0.078 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.04→2.09 Å / Rmerge(I) obs: 0.657 / Num. unique obs: 4041 / Rpim(I) all: 0.637 / Rrim(I) all: 0.918 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→45.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.933 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.153 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.968 Å2
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Refinement step | Cycle: 1 / Resolution: 2.04→45.82 Å
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Refine LS restraints |
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