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Yorodumi- PDB-4uwq: Crystal structure of the disulfide-linked complex of the thiosulf... -
+Open data
-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 | ||||||
Components |
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Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information nucleotide catabolic process / hydrolase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å | ||||||
Authors | Grabarczyk, D.B. / Chappell, P.E. / Johnson, S. / Stelzl, L.S. / Lea, S.M. / Berks, B.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uwq.cif.gz | 568.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uwq.ent.gz | 466.4 KB | Display | PDB format |
PDBx/mmJSON format | 4uwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uwq ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uwq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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.) THERMUS THERMOPHILUS HB27 (bacteria) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): STAR / References: UniProt: Q72IT0 #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.) THERMUS THERMOPHILUS HB27 (bacteria) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): STAR / References: UniProt: Q72IS6 #3: Protein | Mass: 11864.509 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS HB27 (bacteria) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): STAR / References: UniProt: Q72IS7 #4: Chemical | ChemComp-MN / #5: 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: 2.87 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9999 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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