+Open data
-Basic information
Entry | Database: PDB / ID: 3iqm | ||||||
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Title | Active site mutants of B. subtilis SecA | ||||||
Components | Protein translocase subunit secA | ||||||
Keywords | PROTEIN TRANSPORT / alpha-beta protein / ATP-binding / Cell membrane / Membrane / Metal-binding / Nucleotide-binding / Translocation / Transport | ||||||
Function / homology | Function and homology information protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting / membrane raft / ATP binding / metal ion binding ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Kim, D. / Hunt, J.F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: ATPase Active-Site Electrostatic Interactions Control the Global Conformation of the 100 kDa SecA Translocase. Authors: Kim, D.M. / Zheng, H. / Huang, Y.J. / Montelione, G.T. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iqm.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iqm.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 3iqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iqm ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iqm | HTTPS FTP |
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-Related structure data
Related structure data | 3iqyC 1m6nS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | AUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION. |
-Components
#1: Protein | Mass: 91392.773 Da / Num. of mol.: 1 / Fragment: UNP residues 1-802 / Mutation: E208Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU35300, div+, secA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28366 | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.13 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 mM BES pH 7.0, 2.12 M Ammonium sulfate, 31% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 299K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9805 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9805 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→30 Å / Num. all: 20687 / Num. obs: 19343 / % possible obs: 93.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 84 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.047 / Net I/σ(I): 14.92 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2064 / Rsym value: 0.404 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M6N Resolution: 3.4→19.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 161243.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.5609 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.52 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 10
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