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Yorodumi- PDB-9c89: Crystal structure of outer membrane lipoprotein carrier protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c89 | |||||||||
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Title | Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Ehrlichia chaffeensis | |||||||||
Components | Outer membrane lipoprotein carrier protein LolA | |||||||||
Keywords | LIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / LolA | |||||||||
Function / homology | Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / outer membrane-bounded periplasmic space / membrane / Outer membrane lipoprotein carrier protein LolA Function and homology information | |||||||||
Biological species | Ehrlichia chaffeensis str. Arkansas (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Ehrlichia chaffeensis Authors: Lovell, S. / Cooper, A. / Buchko, G.W. / Battaile, K.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c89.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c89.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 9c89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c89_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 9c89_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 9c89_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 9c89_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/9c89 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/9c89 | HTTPS FTP |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22168.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ehrlichia chaffeensis str. Arkansas (bacteria) Gene: ECH_1053 / Plasmid: EhchA.17554.a.VL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2GFE5 |
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-Non-polymers , 5 types, 10 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-PG4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 4.23 Å3/Da / Density % sol: 70.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Index HT C11 + 10% Hampton Additive E5: 1 M ammonium sulfate, 100 mM Hepes pH 7.0, 0.5% (w/v) PEG 8000, 1% (w/v) PEG 3350, EhchA.17554.a.VL2.PK00002 at 3.7 mg/mL. plate 13803 well E5 drop 1. ...Details: Index HT C11 + 10% Hampton Additive E5: 1 M ammonium sulfate, 100 mM Hepes pH 7.0, 0.5% (w/v) PEG 8000, 1% (w/v) PEG 3350, EhchA.17554.a.VL2.PK00002 at 3.7 mg/mL. plate 13803 well E5 drop 1. Puck: PSL-0312, Cryo: 80% crystallant + 20% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2024 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 3→43.72 Å / Num. obs: 7533 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.066 / Rrim(I) all: 0.204 / Χ2: 1.01 / Net I/σ(I): 8.7 / Num. measured all: 73361 |
Reflection shell | Resolution: 3→3.18 Å / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 1.317 / Num. measured all: 13177 / Num. unique obs: 1218 / CC1/2: 0.702 / Rpim(I) all: 0.419 / Rrim(I) all: 1.383 / Χ2: 0.94 / Net I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→43.72 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→43.72 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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