+Open data
-Basic information
Entry | Database: PDB / ID: 4v3g | ||||||
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Title | Crystal structure of CymA from Klebsiella oxytoca | ||||||
Components | CYMA PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / OUTER MEMBRANE CHANNEL CYCLODEXTRIN TRANSPORT BETA BARREL MONOMER | ||||||
Function / homology | Cyclodextrin porin CymA / Putative cyclodextrin porin / import into cell / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / CymA protein Function and homology information | ||||||
Biological species | KLEBSIELLA OXYTOCA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.513 Å | ||||||
Authors | van den Berg, B. / Bhamidimarri, S.P. / Kleinekathoefer, U. / Winterhalter, M. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015 Title: Outer-membrane translocation of bulky small molecules by passive diffusion. Authors: van den Berg, B. / Prathyusha Bhamidimarri, S. / Dahyabhai Prajapati, J. / Kleinekathofer, U. / Winterhalter, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v3g.cif.gz | 284.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v3g.ent.gz | 241.5 KB | Display | PDB format |
PDBx/mmJSON format | 4v3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v3g_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4v3g_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4v3g_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 4v3g_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/4v3g ftp://data.pdbj.org/pub/pdb/validation_reports/v3/4v3g | HTTPS FTP |
-Related structure 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: 39999.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CLONING REGION INCLUDING HEPTAHISTIDINE TAG AT N-TERMINUS Source: (gene. exp.) KLEBSIELLA OXYTOCA (bacteria) / Plasmid: PB22 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): C43 / Variant (production host): DELTA CYOABCD / References: UniProt: Q48391 #2: Chemical | ChemComp-C8E / ( #3: Water | ChemComp-HOH / | Nonpolymer details | (HYDROXYETH | Sequence details | METHIONINE | |
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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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: MOLECULAR DIMENSIONS MORPHEUS 1/35 OPTIMIZED, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 32944 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 59.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.513→48.998 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 27.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.513→48.998 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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