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Yorodumi- PDB-3mqz: Crystal Structure of Conserved Protein DUF1054 from Pink Subaeria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mqz | ||||||
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Title | Crystal Structure of Conserved Protein DUF1054 from Pink Subaerial Biofilm Microbial Leptospirillum sp. Group II UBA. | ||||||
Components | uncharacterized Conserved Protein DUF1054 | ||||||
Keywords | structural genomics / unknown function / alpha-beta fold / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Protein of unknown function DUF1054 / BirA Bifunctional Protein; domain 2 / 2-Layer Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Leptospirillum rubarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Kim, Y. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Conserved Protein DUF1054 from Pink Subaerial Biofilm Microbial Leptospirillum sp. Group II UBA. Authors: Kim, Y. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mqz.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mqz.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/3mqz ftp://data.pdbj.org/pub/pdb/validation_reports/mq/3mqz | 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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Unit cell |
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-Components
#1: Protein | Mass: 24662.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospirillum rubarum (bacteria) / Gene: UBAL2_82410687 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: A3ER16 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 1.88 Å3/Da / Density % sol: 34.42 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2M Sodium Formate, 20%PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 4, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 44135 / Num. obs: 44135 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.056 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.287 / % possible all: 59.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→27.015 Å / SU ML: 0.16 / Isotropic thermal model: anisotropic / σ(F): 1.35 / Phase error: 14.72 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.3→27.015 Å
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Refine LS restraints |
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LS refinement shell |
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