Yorodumi+
Open data
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Basic information
| Entry | Database: PDB / ID: 3sbx | ||||||
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| Title | Crystal structure of a putative uncharacterized protein from Mycobacterium marinum bound to adenosine 5'-monophosphate AMP | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / putative uncharacterized protein / Molybdenum cofactor binding protein / Moco / GTP / orthologs are possible misannotated as possible or putative lysine decarboxylases / AMP was MS verified / proteomics | ||||||
| Function / homology | Function and homology informationcytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process / nucleotide binding / cytosol Similarity search - Function | ||||||
| Biological species | Mycobacterium marinum M (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Tuberculosis (Edinb) / Year: 2015Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 3sbx.cif.gz | 528.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb3sbx.ent.gz | 437.9 KB | Display | PDB format |
| PDBx/mmJSON format | 3sbx.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 3sbx_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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| Full document | 3sbx_full_validation.pdf.gz | 2.6 MB | Display | |
| Data in XML | 3sbx_validation.xml.gz | 53.2 KB | Display | |
| Data in CIF | 3sbx_validation.cif.gz | 70.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/3sbx ftp://data.pdbj.org/pub/pdb/validation_reports/sb/3sbx | 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 ![]() 3quaSC ![]() 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 ![]() 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 ![]() 4hdtC ![]() 4hr3C ![]() 4i1yC ![]() 4ijnC ![]() 4iv6C ![]() 4iz9C ![]() 4j5iC ![]() 4kamC ![]() 4lgvC ![]() 4o2dC S: Starting model for refinement 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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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 11 - 186 / Label seq-ID: 14 - 189
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Components
| #1: Protein | Mass: 20160.760 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: ATCC BAA-535 / M / Gene: MMAR_4233 / Plasmid: pAVA0421 / Production host: ![]() #2: Chemical | ChemComp-AMP / #3: 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: 2.71 Å3/Da / Density % sol: 54.54 % |
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| Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: MymaA.00620.b.A1 PW29922 at 27.2 mg/mL against JCSG+ screen condition C1, 0.2 M NaCl, 0.1 M phosphate/citrate pH 4.2, 20% PEG 8000 with 25% ethylene glycol as cryo-protection reagent, ...Details: MymaA.00620.b.A1 PW29922 at 27.2 mg/mL against JCSG+ screen condition C1, 0.2 M NaCl, 0.1 M phosphate/citrate pH 4.2, 20% PEG 8000 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 218867c1, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
| Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection | Resolution: 2.5→50 Å / Num. all: 58548 / Num. obs: 52931 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.16 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection shell |
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-Phasing
| Phasing | Method: molecular replacement | |||||||||
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| Phasing MR | Rfactor: 47.43 / Model details: Phaser MODE: MR_AUTO
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 3QUA Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.87 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 25.291 / SU ML: 0.26 / SU R Cruickshank DPI: 0.7924 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.351 / 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: 34.994 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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| Refine LS restraints |
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| Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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Movie
Controller
About Yorodumi



Mycobacterium marinum M (bacteria)
X-RAY DIFFRACTION
Citation







































































































































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