+Open data
-Basic information
Entry | Database: PDB / ID: 4au5 | ||||||
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Title | Structure of the NhaA dimer, crystallised at low pH | ||||||
Components | NA(+)/H(+) ANTIPORTER NHAA | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORTER | ||||||
Function / homology | Function and homology information response to alkaline pH / sodium:proton antiporter activity / cardiolipin binding / response to salt stress / regulation of intracellular pH / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.696 Å | ||||||
Authors | Drew, D. / Lee, C. / Iwata, S. / Cameron, A.D. | ||||||
Citation | Journal: J. Gen. Physiol. / Year: 2014 Title: Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights. Authors: Lee, C. / Yashiro, S. / Dotson, D.L. / Uzdavinys, P. / Iwata, S. / Sansom, M.S. / von Ballmoos, C. / Beckstein, O. / Drew, D. / Cameron, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4au5.cif.gz | 590.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4au5.ent.gz | 496.4 KB | Display | PDB format |
PDBx/mmJSON format | 4au5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4au5_validation.pdf.gz | 729.7 KB | Display | wwPDB validaton report |
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Full document | 4au5_full_validation.pdf.gz | 760.7 KB | Display | |
Data in XML | 4au5_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 4au5_validation.cif.gz | 74.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/4au5 ftp://data.pdbj.org/pub/pdb/validation_reports/au/4au5 | HTTPS FTP |
-Related structure data
Related structure data | 4atvSC 1zcdS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 42957.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWALDO GFPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P13738 #2: Sugar | ChemComp-LMU / | #3: Chemical | ChemComp-SO4 / |
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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: 4.8 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | pH: 3.8 Details: 0.1 M SODIUM CITRATE PH 3.8, 0.1 M LITHIUM SULPHATE, 26% PEG 400 WITH 1% HEPTYL-THIOL-B-D-GLUCOSIDE AS AN ADDITIVE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 |
Detector | Type: MARRESEARCH MX300 / Detector: CCD / Date: Apr 24, 2009 |
Radiation | Monochromator: SI(III) DOUBLE CRYSTAL MONOCHOMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→30 Å / Num. obs: 34273 / % possible obs: 98.1 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 133.33 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.7→3.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.2 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZCD -FINAL REFINEMENT DONE AGAINST 4ATV Resolution: 3.696→29.644 Å / SU ML: 0.6 / σ(F): 1.38 / Phase error: 43.16 / Stereochemistry target values: ML Details: RESTRAINED TO 4ATV USED SECONDARY STRUCTURE AND NCS RESTRAINTS. REFINED WITH NCS RESTRAINTS AND RESTRAINED TO 4ATV. SULPHATE AND DETERGENT TENTATIVELY MODELLED IN DIMER INTERFACE AS FOR 4ATV.
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.901 Å2 / ksol: 0.186 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 205 Å2
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Refinement step | Cycle: LAST / Resolution: 3.696→29.644 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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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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