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- PDB-4uwq: Crystal structure of the disulfide-linked complex of the thiosulf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uwq | ||||||
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Title | Crystal structure of the disulfide-linked complex of the thiosulfodyrolase SoxB with the carrier-protein SoxYZ from Thermus thermophilus | ||||||
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![]() | HYDROLASE | ||||||
Function / homology | ![]() nucleotide catabolic process / outer membrane-bounded periplasmic space / hydrolase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grabarczyk, D.B. / Chappell, P.E. / Johnson, S. / Stelzl, L.S. / Lea, S.M. / Berks, B.C. | ||||||
![]() | ![]() Title: Structural Basis for Specificity and Promiscuity in a Carrier Protein/Enzyme System from the Sulfur Cycle Authors: Grabarczyk, D.B. / Chappell, P.E. / Johnson, S. / Stelzl, L.S. / Lea, S.M. / Berks, B.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 568.4 KB | Display | ![]() |
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PDB format | ![]() | 466.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 545.9 KB | Display | ![]() |
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Full document | ![]() | 586 KB | Display | |
Data in XML | ![]() | 93 KB | Display | |
Data in CIF | ![]() | 126.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 62664.371 Da / Num. of mol.: 4 / Fragment: RESIDUES 23-573 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14718.761 Da / Num. of mol.: 4 / Fragment: RESIDUES 29-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 11864.509 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | ChemComp-MN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.18 % / Description: NONE |
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Crystal grow | pH: 8.3 Details: 0.1M TRIS-HCL, 0.2M (NH4)2SO4, 8.55% PEG 8000, PH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 3.28→59.81 Å / Num. obs: 112492 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 90.37 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.28→3.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.9 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2WDF, 1V8H AND AN UNPUBLISHED SOXY STRUCTURE Resolution: 3.28→59.81 Å / Cor.coef. Fo:Fc: 0.8229 / Cor.coef. Fo:Fc free: 0.827 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.543 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=23073. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=23073. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
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Displacement parameters | Biso mean: 92.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.855 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.28→59.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.28→3.37 Å / Total num. of bins used: 20
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