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- PDB-4hdt: Crystal structure of a Carnitinyl-CoA dehydratase from Mycobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hdt | ||||||
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Title | Crystal structure of a Carnitinyl-CoA dehydratase from Mycobacterium thermoresistibile | ||||||
![]() | 3-hydroxyisobutyryl-CoA hydrolase | ||||||
![]() | ISOMERASE / SSGCID / Carnitinyl-CoA dehydratase / Enoyl-CoA hydratase/isomerase / Mycobacterium thermoresistibile / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Increasing the structural coverage of tuberculosis drug targets. Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.3 KB | Display | ![]() |
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PDB format | ![]() | 111.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.4 KB | Display | ![]() |
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Full document | ![]() | 424.8 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gvcC ![]() 3gvgC ![]() 3gwcC ![]() 3h7fC ![]() 3h81C ![]() 3he2C ![]() 3hwiC ![]() 3hwkC ![]() 3hzgC ![]() 3icoC ![]() 3khpC ![]() 3llsC ![]() 3moyC ![]() 3mpzC ![]() 3mybC ![]() 3ndnC ![]() 3ndoC ![]() 3nf4C ![]() 3ng3C ![]() 3njdC ![]() 3nwoC ![]() 3o0mC ![]() 3o38C ![]() 3oc6C ![]() 3oc7C ![]() 3oi9C ![]() 3oksC ![]() 3omeC ![]() 3p0tC ![]() 3p2yC ![]() 3p4iC ![]() 3p4tC ![]() 3p5mC ![]() 3p85C ![]() 3pe8C ![]() 3pk0C ![]() 3ppiC ![]() 3pzyC ![]() 3q1tC ![]() 3q8nC ![]() 3qbpC ![]() 3qdfC ![]() 3qhaC ![]() 3qivC ![]() 3qk8C ![]() 3qkaC ![]() 3qljC ![]() 3qmjC ![]() 3qreC ![]() 3quaC ![]() 3quvC ![]() 3qxiC ![]() 3qxzC ![]() 3qyrC ![]() 3r0oC ![]() 3r1iC ![]() 3r1jC ![]() 3r20C ![]() 3r2nC ![]() 3r4tC ![]() 3r6hC ![]() 3r6oC ![]() 3r7kC ![]() 3r8cC ![]() 3r9pC ![]() 3r9qC ![]() 3r9rC ![]() 3r9sC ![]() 3r9tC ![]() 3rd5C ![]() 3rd7C ![]() 3rd8C ![]() 3rfqC ![]() 3rihC ![]() 3rr2C ![]() 3rr6C ![]() 3rrpC ![]() 3rrvC ![]() 3rsiC ![]() 3rv2C ![]() 3s82C ![]() 3sbxC ![]() 3sf6C ![]() 3sllC ![]() 3svkC ![]() 3svtC ![]() 3swoC ![]() 3swtC ![]() 3swxC ![]() 3t3wC ![]() 3tavC ![]() 3tcrC ![]() 3tdeC ![]() 3tjrC ![]() 3tl3C ![]() 3tlfC ![]() 3trrC ![]() 3tx2C ![]() 3tzqC ![]() 3tzuC ![]() 3u0aC ![]() 3ucxC ![]() 3uveC ![]() 4di1C ![]() 4dieC ![]() 4dq8C ![]() 4dxlC ![]() 4ed4C ![]() 4egeC ![]() 4egfC ![]() 4emdC ![]() 4eo9C ![]() 4eyeC ![]() 4f3wC ![]() 4f47C ![]() 4ffcC ![]() 4gk6C ![]() 4hr3C ![]() 4i1yC ![]() 4ijnC ![]() 4iv6C ![]() 4iz9C ![]() 4j5iC ![]() 4kamC ![]() 4lgvC ![]() 4o2dC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37525.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 19527 / NCTC 10409 / Gene: KEK_02971, NODE_1249_length_5618_cov_9.770559_39 / Plasmid: AVA0421 / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5 Details: EMBioPACT screen A12: 10mM ZnCl2, 100mM NaOAc pH 5.0, 20% PEG 6000; MythA.01530.a.A1.PW28690 at 29mg/ml; 25% EG as cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 157472 / Rmerge(I) obs: 0.042 / D res high: 1.6 Å / Num. obs: 80460 / % possible obs: 97.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.6→50 Å / Num. all: 42068 / Num. obs: 41586 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 22.954 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.77 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Phasing MAD | D res high: 1.6 Å / D res low: 45.41 Å / FOM : 0.323 / FOM acentric: 0.33 / FOM centric: 0.168 / Reflection: 41571 / Reflection acentric: 38854 / Reflection centric: 1533 |
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Processing
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Refinement | Method to determine structure: Zn-SAD / Resolution: 1.6→45.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1752 / WRfactor Rwork: 0.1495 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8907 / SU B: 3.014 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0824 / SU Rfree: 0.0825 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.08 Å2 / Biso mean: 17.9527 Å2 / Biso min: 7.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→45.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 2.007 Å / Origin y: 29.574 Å / Origin z: 43.971 Å
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Refinement TLS group |
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