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Yorodumi- PDB-2guk: Crystal Structure of the Conserved Protein of Unknown Function fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2guk | ||||||
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Title | Crystal Structure of the Conserved Protein of Unknown Function from Porphyromonas gingivalis | ||||||
Components | hypothetical protein PG1857 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta / alpha-helical bundle / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | PG1857-like / PG1857-like / Domain of unknown function DUF2023 / PG1857-like superfamily / Protein of unknown function (DUF2023) / 2-Layer Sandwich / Alpha Beta / : / DUF2023 domain-containing protein Function and homology information | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Kim, Y. / Quartey, P. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Conserved Hypothetical Protein from Porphyromonas gingivalis Authors: Kim, Y. / Quartey, P. / Moy, S. / Joachimiak, A. | ||||||
History |
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Remark 300 | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THERE IS NO ...THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THERE IS NO EXPERIMENTAL EVIDENCE ABOUT THE BIOLOGICAL UNIT. THE BIOLOGICAL UNIT COULD BE A DIMER (AS IN THE ASYMMETRIC UNIT) OR A TETRAMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2guk.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2guk.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 2guk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2guk_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 2guk_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 2guk_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2guk_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/2guk ftp://data.pdbj.org/pub/pdb/validation_reports/gu/2guk | 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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-Components
#1: Protein | Mass: 14193.339 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG1587, GeneID:2551814 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 34541468, UniProt: Q7MTT4*PLUS #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: 2.06 Å3/Da / Density % sol: 40.27 % |
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Crystal grow | Temperature: 275 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5% iso-propanol, 0.1 M HEPES 7.5, 10 % PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 275K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2006 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→34.76 Å / Num. all: 20138 / Num. obs: 19279 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1825 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→34.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.435 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.22 / ESU R Free: 0.192 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.333 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→34.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Total num. of bins used: 20
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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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