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Yorodumi- PDB-2p0s: Structural Genomics, the crystal structure of a putative ABC tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p0s | ||||||
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Title | Structural Genomics, the crystal structure of a putative ABC transporter domain from Porphyromonas gingivalis W83 | ||||||
Components | ABC transporter, permease protein, putative | ||||||
Keywords | TRANSPORT PROTEIN / APC90123.1 / putative ABC transporter / Porphyromonas gingivalis W83 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / membrane => GO:0016020 / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / FORMIC ACID / ABC transporter, permease protein, putative Function and homology information | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Tan, K. / Duggan, E. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a putative ABC transporter domain from Porphyromonas gingivalis W83 Authors: Tan, K. / Duggan, E. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN AND THE ASSEMBLY OF THE BIOLOGICAL UNIT SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p0s.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p0s.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 2p0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p0s_validation.pdf.gz | 458.8 KB | Display | wwPDB validaton report |
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Full document | 2p0s_full_validation.pdf.gz | 462.1 KB | Display | |
Data in XML | 2p0s_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2p0s_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/2p0s ftp://data.pdbj.org/pub/pdb/validation_reports/p0/2p0s | HTTPS FTP |
-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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Details | Experimentally unknown. Based on the structure, the chains A and B likely form a dimer. |
-Components
#1: Protein | Mass: 16073.492 Da / Num. of mol.: 2 / Fragment: One domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0945 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7MVU4 #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: 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: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M MgCl2, 0.1M NaCl, 30% PEG400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2006 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.56 Å / Num. all: 31663 / Num. obs: 31663 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 43.87 |
Reflection shell | Resolution: 1.6→1.62 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.35 / Num. unique all: 848 / % possible all: 66.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→40.56 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.394 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.337 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→40.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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