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Yorodumi- PDB-3zxq: CRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBE... -
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-Basic information
Entry | Database: PDB / ID: 3zxq | ||||||
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Title | CRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOST | ||||||
Components | HYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOST | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information detection of hypoxia / protein histidine kinase activity / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / oxygen binding / protein autophosphorylation ...detection of hypoxia / protein histidine kinase activity / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / oxygen binding / protein autophosphorylation / protein dimerization activity / protein kinase activity / calcium ion binding / heme binding / magnesium ion binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cho, H.Y. / Cho, H.J. / Kang, B.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Activation of ATP Binding for the Autophosphorylation of Doss, a Mycobacterium Tuberculosis Histidine Kinase Lacking an ATP-Lid Motif. Authors: Cho, H.Y. / Lee, Y.H. / Bae, Y.S. / Kim, E. / Kang, B.S. #1: Journal: J.Mol.Biol. / Year: 2005 Title: A Gaf Domain in the Hypoxia/No-Inducible Mycobacterium Tuberculosis Doss Protein Binds Haem. Authors: Sardiwal, S. / Kendall, S.L. / Movahedzadeh, F. / Rison, S.C.G. / Stoker, N.G. / Djordjevic, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zxq.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zxq.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zxq_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
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Full document | 3zxq_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 3zxq_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3zxq_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/3zxq ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxq | HTTPS FTP |
-Related structure data
Related structure data | 3zxoSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13262.812 Da / Num. of mol.: 2 / Fragment: ATP-BINDING DOMAIN, RESIDUES 451-573 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53473, UniProt: P9WGK1*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | T451 TO Q573 OF DOSS WITH ADDITIONAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.2 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.5 M SODIUM CHLORIDE, 10% ETHANOL, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 2, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 37177 / % possible obs: 99.7 % / Observed criterion σ(I): -2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.95 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.18 / % possible all: 92.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZXO Resolution: 1.9→31.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.121 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 19.349 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→31.83 Å
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