[English] 日本語
Yorodumi- PDB-3nfw: Crystal structure of nitrilotriacetate monooxygenase component B ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nfw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of nitrilotriacetate monooxygenase component B (A0R521 homolog) from Mycobacterium thermoresistibile | ||||||
Components | Flavin reductase-like, FMN-binding protein | ||||||
Keywords | OXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / tuberculosis / thermoresistible / biodegredation / NADH dependent | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / monooxygenase activity / FMN binding Similarity search - Function | ||||||
Biological species | Mycobacterium thermoresistibile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structure of nitrilotriacetate monooxygenase component B from Mycobacterium thermoresistibile. Authors: Zhang, Y. / Edwards, T.E. / Begley, D.W. / Abramov, A. / Thompkins, K.B. / Ferrell, M. / Guo, W.J. / Phan, I. / Olsen, C. / Napuli, A. / Sankaran, B. / Stacy, R. / Van Voorhis, W.C. / Stewart, L.J. / Myler, P.J. #1: Journal: Tuberculosis (Edinb) / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3nfw.cif.gz | 285 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3nfw.ent.gz | 230 KB | Display | PDB format |
PDBx/mmJSON format | 3nfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nfw_validation.pdf.gz | 465 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3nfw_full_validation.pdf.gz | 467 KB | Display | |
Data in XML | 3nfw_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 3nfw_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/3nfw ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nfw | HTTPS FTP |
-Related structure data
Related structure data | 1rz0S S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23307.271 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: G7CEX2, UniProt: E5Q9D7*PLUS #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.21 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 68.9 mg/mL protein against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 20% glycerol as cryo-protectant, crystal tracking ID 215735b10, VAPOR DIFFUSION, ...Details: 68.9 mg/mL protein against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 20% glycerol as cryo-protectant, crystal tracking ID 215735b10, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 97543 / Num. obs: 97350 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.5 % / Biso Wilson estimate: 20.998 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 61.42 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1rz0 Resolution: 1.6→19.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2239 / WRfactor Rwork: 0.1915 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8626 / SU B: 3.142 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0913 / SU Rfree: 0.0913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 58.9 Å2 / Biso mean: 16.7061 Å2 / Biso min: 5.32 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.56 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|