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Yorodumi- PDB-3fxe: Crystal structure of interacting domains of IcmR and IcmQ (seleno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fxe | ||||||
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Title | Crystal structure of interacting domains of IcmR and IcmQ (seleno-derivative) | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / 4 helix bundle / helix-turn-helix / Se-Met | ||||||
Function / homology | Function and homology information : / IcmR, middle region / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Immunoglobulin FC, subunit C / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Legionella pneumophila (bacteria) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Raychaudhury, S. / Akey, C.W. / Head, J.F. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structure and Function of Interacting IcmR-IcmQ Domains from a Type IVb Secretion System in Legionella pneumophila. Authors: Raychaudhury, S. / Farelli, J.D. / Montminy, T.P. / Matthews, M. / Menetret, J.F. / Dumenil, G. / Roy, C.R. / Head, J.F. / Isberg, R.R. / Akey, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fxe.cif.gz | 28.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fxe.ent.gz | 22 KB | Display | PDB format |
PDBx/mmJSON format | 3fxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fxe_validation.pdf.gz | 417.9 KB | Display | wwPDB validaton report |
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Full document | 3fxe_full_validation.pdf.gz | 419.3 KB | Display | |
Data in XML | 3fxe_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 3fxe_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/3fxe ftp://data.pdbj.org/pub/pdb/validation_reports/fx/3fxe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6557.525 Da / Num. of mol.: 1 / Fragment: UNP residues 1-57 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: icmQ, LPC_2899 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: A5IHF0 |
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#2: Protein | Mass: 7859.662 Da / Num. of mol.: 1 / Fragment: UNP residues 23-95 / Mutation: L84M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia-1 / DSM 7513 / Gene: icmR, lpg0443 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Xl-1 blue / References: UniProt: Q5ZYC9 |
#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: 1.8 Å3/Da / Density % sol: 31.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 100 mM Na acetate pH 4.7, 30% PEG 1500, 100 mM L-cysteine, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97950, 0.97976, 0.95003 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 10, 2004 | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. all: 10087 / Num. obs: 10087 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.9 | ||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 18 / Num. unique all: 541 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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