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Open data
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Basic information
Entry | Database: PDB / ID: 7u1b | ||||||
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Title | Crystal structure of EstG in complex with tantalum cluster | ||||||
![]() | Beta-lactamase domain-containing protein | ||||||
![]() | HYDROLASE / alpha/beta fold / CCNA_01638 | ||||||
Function / homology | Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / HEXATANTALUM DODECABROMIDE / Beta-lactamase-related domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Z. / Gabelli, S.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: EstG is a novel esterase required for cell envelope integrity in Caulobacter. Authors: Daitch, A.K. / Orsburn, B.C. / Chen, Z. / Alvarez, L. / Eberhard, C.D. / Sundararajan, K. / Zeinert, R. / Kreitler, D.F. / Jakoncic, J. / Chien, P. / Cava, F. / Gabelli, S.B. / Goley, E.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.8 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.6 KB | Display | ![]() |
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Full document | ![]() | 496.2 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u1cC ![]() 7udaC ![]() 1ci8S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 49922.344 Da / Num. of mol.: 1 Fragment: estG, Esterase for Stress Tolerance acting on glucans Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 14 molecules ![](data/chem/img/TBR.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-TBR / |
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#3: Chemical | ChemComp-BCN / |
#4: Chemical | ChemComp-TRS / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.21 % / Mosaicity: 0.13 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: 20% PEG500 MME, 10% PEG20000, 0.1 M Tris/Bicine pH 8.5 and 90 mM mixture of sodium nitrate, sodium phosphate dibasic and ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 16, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92009 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.62→28.71 Å / Num. obs: 21379 / % possible obs: 99.5 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.037 / Rrim(I) all: 0.113 / Net I/σ(I): 16.9 / Num. measured all: 195511 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CI8 Resolution: 2.62→27.96 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2133 / WRfactor Rwork: 0.1755 / FOM work R set: 0.8299 / SU B: 8.745 / SU ML: 0.177 / SU R Cruickshank DPI: 0.3214 / SU Rfree: 0.2455 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 420.63 Å2 / Biso mean: 49.622 Å2 / Biso min: 25.32 Å2
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Refinement step | Cycle: final / Resolution: 2.62→27.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.625→2.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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