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Yorodumi- PDB-1x9j: Structure of butyrate kinase 2 reveals both open- and citrate-ind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x9j | ||||||
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Title | Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes | ||||||
Components | Probable butyrate kinase 2 | ||||||
Keywords | TRANSFERASE / ASKHA (ACETATE AND SUGAR KINASES / HSC70 / ACTIN) SUPERFAMILY / BUTYRATE KINASE / ACETATE KINASE / ISOBUTYRATE KINASE / TWO SIMILAR DOMAINS / BUTYRATE / ISOBUTYRATE / ENZYME MECHANISM | ||||||
Function / homology | Function and homology information butyrate kinase / butyrate kinase activity / acetate kinase activity / acetate metabolic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Diao, J.S. / Sanders, D.A. / Hasson, M.S. | ||||||
Citation | Journal: To be Published Title: Structure of butyrate kinase 2 reveals both open and closed conformations of the two domains: implications for substrate-induced changes Authors: Diao, J.S. / Bhattacharyya, S. / Ma, Y.L.D. / Sanders, D.A. / Hasson, M.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization of Butyrate Kinase 2 from Thermotoga Maritima Mediated by Vapour Diffusion of Acetic Acid Authors: Diao, J.S. / Cooper, D.R. / Sanders, D.A. / Hasson, M.S. #2: Journal: To be Published Title: Membership in the Askha Superfamily: Enzymological Properties and Crystal Structure of Butyrate Kinase 2 from Thermotoga Maritima Authors: Diao, J.S. / Cooper, D.R. / Bhattacharyya, S. / Sanders, D.A. / Hasson, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x9j.cif.gz | 570.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x9j.ent.gz | 475.7 KB | Display | PDB format |
PDBx/mmJSON format | 1x9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x9j_validation.pdf.gz | 512.6 KB | Display | wwPDB validaton report |
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Full document | 1x9j_full_validation.pdf.gz | 606.5 KB | Display | |
Data in XML | 1x9j_validation.xml.gz | 72.7 KB | Display | |
Data in CIF | 1x9j_validation.cif.gz | 102.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/1x9j ftp://data.pdbj.org/pub/pdb/validation_reports/x9/1x9j | HTTPS FTP |
-Related structure data
Related structure data | 1sazS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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5 |
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Unit cell |
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Details | THE BIOLOGICAL UNIT IS IDENTICAL TO THE ASYMMETRIC UNIT, WHICH IS AN OCTAMER. |
-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 42083.355 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: buk2 / Plasmid: PET30A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q9X278, butyrate kinase |
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-Non-polymers , 5 types, 62 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-CIT / #6: 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: 3.6 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: CRYSTALLIZATION CONDITIONS: THE PROTEIN SOLUTION CONTAINS 22.5-25 mg/ml BUK2, 25 mM TRIS-HCl pH 8.5, 400 mM NACl, 5 mM DTT, 10%(w/v) GLYCEROL. THE RESERVOIR SOLUTION IS 1ml of 77 mM ...Details: CRYSTALLIZATION CONDITIONS: THE PROTEIN SOLUTION CONTAINS 22.5-25 mg/ml BUK2, 25 mM TRIS-HCl pH 8.5, 400 mM NACl, 5 mM DTT, 10%(w/v) GLYCEROL. THE RESERVOIR SOLUTION IS 1ml of 77 mM PHOSPHATE-CITRATE AND 55% (w/v) PEG 200, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9793 / Wavelength: 0.9793 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. all: 88518 / Num. obs: 88350 / % possible obs: 97 % / Redundancy: 14.2 % / Biso Wilson estimate: 68.8 Å2 / Rsym value: 0.093 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 7233 / Rsym value: 0.359 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SAZ Resolution: 3→91.48 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3022342.25 / Data cutoff low absF: 0 / Isotropic thermal model: ISOROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.0944 Å2 / ksol: 0.346204 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.2 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→91.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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