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Yorodumi- PDB-3v4h: Crystal structure of a type VI secretion system effector from Yer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v4h | ||||||
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Title | Crystal structure of a type VI secretion system effector from Yersinia pestis | ||||||
Components | hypothetical protein | ||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Hcp1-like / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / Hcp1 family type VI secretion system effector Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Filippova, E.V. / Halavaty, A. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a type VI secretion system effector from Yersinia pestis Authors: Filippova, E.V. / Halavaty, A. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v4h.cif.gz | 120.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v4h.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 3v4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/3v4h ftp://data.pdbj.org/pub/pdb/validation_reports/v4/3v4h | HTTPS FTP |
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-Related structure data
Related structure data | 1y12S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 20697.156 Da / Num. of mol.: 2 / Fragment: UNP residues 29-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: y1547, YPO2937, YP_2759 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 "magic" / References: UniProt: Q8CLE0 #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: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M Citric acid, 1.4 M Ammonium Sulfate, 25% sucrose, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 20196 / Num. obs: 20196 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.473 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.4 / Num. unique all: 890 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Y12 Resolution: 2.1→29.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.904 / SU ML: 0.169 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.193 / 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: 57.202 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 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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