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Yorodumi- PDB-3jvc: Crystal Structure of the Lipoprotein_17 domain from Q9PRA0_UREPA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jvc | ||||||
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Title | Crystal Structure of the Lipoprotein_17 domain from Q9PRA0_UREPA protein of Ureaplasma parvum. Northeast Structural Genomics Consortium Target UuR17a. | ||||||
Components | Conserved hypothetical membrane lipoprotein | ||||||
Keywords | LIPID BINDING PROTEIN / lipoprotein-17 / Q9PRA0 / PF04200 / DUF1976 / UuR17a / NESG. / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Lipoprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ureaplasma parvum serovar 3 str. ATCC 700970 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å | ||||||
Authors | Vorobiev, S. / Neely, H. / Lee, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Lipoprotein_17 domain from Q9PRA0_UREPA protein of Ureaplasma parvum. Authors: Vorobiev, S. / Neely, H. / Lee, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / 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 | 3jvc.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jvc.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 3jvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/3jvc ftp://data.pdbj.org/pub/pdb/validation_reports/jv/3jvc | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | monomer according to gel-filtration |
-Components
#1: Protein | Mass: 14782.609 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ureaplasma parvum serovar 3 str. ATCC 700970 (bacteria) Strain: ATCC 700970 / Serovar 3 / Gene: UU045 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q9PRA0 #2: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 291 K / Method: microbatch under paraffin oil / pH: 7.5 Details: 24% PEG 20000, 0.1M RbCl, 0.1M HEPES, pH 7.5, microbatch under paraffin oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. all: 22432 / Num. obs: 22095 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 52.2 |
Reflection shell | Resolution: 2.69→2.79 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 14.2 / Num. unique all: 2184 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.69→38.42 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 161344.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.4848 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.69→38.42 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.69→2.86 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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