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Yorodumi- PDB-3kzx: Crystal structure of a Had-superfamily hydrolase from Ehrlichia c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kzx | ||||||
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Title | Crystal structure of a Had-superfamily hydrolase from Ehrlichia chaffeensis at 1.9A resolution | ||||||
Components | HAD-superfamily hydrolase, subfamily IA, variant 1 | ||||||
Keywords | HYDROLASE / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / EHRLICHIA CHAFFEENSIS / HAD-SUPERFAMILY HYDROLASE / ALS collaborative crystallography / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ehrlichia chaffeensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a Had-superfamily hydrolase from Ehrlichia chaffeensis at 1.9A resolution Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Edwards, T.E. / Sankaran, B. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kzx.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kzx.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzx ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzx | HTTPS FTP |
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-Related structure data
Related structure data | 3d6jS 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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Unit cell |
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-Components
#1: Protein | Mass: 26101.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ehrlichia chaffeensis (bacteria) / Strain: Arkansas / Gene: ECH_0332 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GHD1 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: HR INDEX SCREEN C6: 100MM BISTRIS PH 6.5, 1.5M AMMONIUM SULPHATE, 100MM NACL; EHCHA.01190.A AT 27MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 21383 / Num. obs: 21206 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 26.24 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.54 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1531 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3d6j modified with CCP4 program CHAINSAW and trimmed to conserved domain Resolution: 1.9→33.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.898 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: 9.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→33.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 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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