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Yorodumi- PDB-4ifa: 1.5 Angstrom resolution crystal structure of an extracellular pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ifa | ||||||
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Title | 1.5 Angstrom resolution crystal structure of an extracellular protein containing a SCP domain from Bacillus anthracis str. Ames | ||||||
Components | Extracellular protein containing a SCP domainGlossary of biology | ||||||
Keywords | UNKNOWN FUNCTION / extracellular protein containing a SCP domain / vaccine candidate / virulence / pathogenesis / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / alpha/beta fold | ||||||
Function / homology | Function and homology information CAP-associated domain / CAP-associated N-terminal / Pathogenesis-related Protein p14a / CAP / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Shatsman, S. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.5 Angstrom resolution crystal structure of an extracellular protein containing a SCP domain from Bacillus anthracis str. Ames Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Shatsman, S. / Peterson, S.N. / 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 | 4ifa.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ifa.ent.gz | 135.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ifa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/4ifa ftp://data.pdbj.org/pub/pdb/validation_reports/if/4ifa | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39214.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_4147, BAS3849, GBAA_4147 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Magic / References: UniProt: Q81W36, UniProt: A0A348A8R7*PLUS |
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-Non-polymers , 5 types, 499 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / | #4: Chemical | #5: Chemical | #6: 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: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: protein at 7.7 mg/mL in 10 mM Tris-HCL pH 8.3 500 mM NaCl, 5 mM BME, crystallization: The Classics II Suite (condition G11: 200 mM Mg Cl2, 100 mM Bis-Tris pH 6.5, 25% (w/v) PEG3350 , VAPOR ...Details: protein at 7.7 mg/mL in 10 mM Tris-HCL pH 8.3 500 mM NaCl, 5 mM BME, crystallization: The Classics II Suite (condition G11: 200 mM Mg Cl2, 100 mM Bis-Tris pH 6.5, 25% (w/v) PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-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: Dec 10, 2012 / Details: Be Lenses |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 56956 / Num. obs: 56956 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 47 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2809 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→29.67 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.459 / SU ML: 0.042 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.067 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.292 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 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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