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Yorodumi- PDB-2uz0: The Crystal crystal structure of the estA protein, a virulence fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uz0 | ||||||
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Title | The Crystal crystal structure of the estA protein, a virulence factor estA protein from Streptococcus pneumonia | ||||||
Components | TRIBUTYRIN ESTERASE | ||||||
Keywords | HYDROLASE / ESTERASE / ALPHA/BETA HYDROLASE / A VIRULENCE FACTOR FOR LUNG INFECTION | ||||||
Function / homology | Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Tributyrin esterase / Tributyrin esterase Function and homology information | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kim, M.H. / Kang, B.S. / Kim, K.J. / Oh, T.K. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: The Crystal Structure of the Esta Protein, a Virulence Factor from Streptococcus Pneumoniae. Authors: Kim, M.H. / Kang, B.S. / Kim, S. / Kim, K.J. / Lee, C.H. / Oh, B.C. / Park, S.C. / Oh, T.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uz0.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uz0.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 2uz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uz0_validation.pdf.gz | 481.9 KB | Display | wwPDB validaton report |
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Full document | 2uz0_full_validation.pdf.gz | 496.3 KB | Display | |
Data in XML | 2uz0_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 2uz0_validation.cif.gz | 61.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uz0 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uz0 | HTTPS FTP |
-Related structure data
Related structure data | 2cfn |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30599.404 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q97S09, UniProt: A0A0H2UNZ8*PLUS #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % Description: STARTING MODEL FOR MR WAS A PARTIALLY REFINED MODEL OF THE SEMET CRYSTAL AT A 1.9A. |
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Crystal grow | Details: 10% (V/V) PEG 6000,8% (V/V) ETHYLENE GLYCOL,4% (V/V) 2-METHYL-2,4-PENTANEDIOL,10 MM CYSTEINE,0.1 M TRIS-HCL PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 113097 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.949 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / 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: 20.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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