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Yorodumi- PDB-3sxk: Zn2+-bound FCD domain of TM0439, a putative transcriptional regulator -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sxk | ||||||
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Title | Zn2+-bound FCD domain of TM0439, a putative transcriptional regulator | ||||||
Components | Transcriptional regulator, GntR family | ||||||
Keywords | TRANSCRIPTION REGULATOR / TRANSCRIPTION FACTOR / TRANSCRIPTION / METAL-BINDING / Structural Genomics / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / FADR-C / FADR / GNTR / TRANSCRIPTIONAL REGULATOR / TRANSCRIPTION REPRESSOR / ZINC-BINDING / NICKEL-BINDING / DNA-BINDING / SURFACE ENTROPY REDUCTION | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Czelakowski, G.P. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI) | ||||||
Citation | Journal: To be Published Title: Zn2+-bound FCD domain of TM0439, a putative transcriptional regulator Authors: Czelakowski, G.P. / Derewenda, Z.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. Authors: Zheng, M. / Cooper, D.R. / Grossoehme, N.E. / Yu, M. / Hung, L.W. / Cieslik, M. / Derewenda, U. / Lesley, S.A. / Wilson, I.A. / Giedroc, D.P. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sxk.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sxk.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 3sxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sxk ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sxk | HTTPS FTP |
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-Related structure data
Related structure data | 3fmsS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.536423, 0.006519, 0.843924), Vector: Details | biological unit is the same as asym. | |
-Components
#1: Protein | Mass: 16459.686 Da / Num. of mol.: 2 / Fragment: Sequence database residues 75-211 / Mutation: E118A, K119A, K122A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0439 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYS0 #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #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: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50 mM Tris pH 8.0, 100 mM NaCl, 200 mM (NH4)2SO4, 100 mM BisTris pH 5.5, 25% PEG 3350, 0.1 mM ZnCl2, 2 mM DTT , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2010 / Details: Mirrors Rh/Pt coated | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.63→45 Å / Num. all: 39975 / Num. obs: 38096 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.041 / Χ2: 1.012 / Net I/σ(I): 26.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB: 3FMS, Chain A: 72-211 Resolution: 1.63→39.922 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8657 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 20.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.428 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.25 Å2 / Biso mean: 27.8605 Å2 / Biso min: 9.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→39.922 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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