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- PDB-1kll: Molecular basis of mitomycin C resictance in streptomyces: Crysta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kll | ||||||
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Title | Molecular basis of mitomycin C resictance in streptomyces: Crystal structures of the MRD protein with and without a drug derivative | ||||||
![]() | mitomycin-binding protein | ||||||
![]() | ANTIMICROBIAL PROTEIN / Mitomycin C / antibiotic resistance / SAD / anomalous diffraction / domain swapping / p-staking | ||||||
Function / homology | ![]() 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Martin, T.W. / Dauter, Z. / Devedjiev, Y. / Sheffield, P. / Jelen, F. / He, M. / Sherman, D. / Otlewski, J. / Derewenda, Z.S. / Derewenda, U. | ||||||
![]() | ![]() Title: Molecular basis of mitomycin C resistance in streptomyces: structure and function of the MRD protein. Authors: Martin, T.W. / Dauter, Z. / Devedjiev, Y. / Sheffield, P. / Jelen, F. / He, M. / Sherman, D.H. / Otlewski, J. / Derewenda, Z.S. / Derewenda, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88 KB | Display | ![]() |
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PDB format | ![]() | 73.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.9 KB | Display | ![]() |
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Full document | ![]() | 726.6 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the crystallographic two fold axis |
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Components
#1: Protein | Mass: 14571.889 Da / Num. of mol.: 1 / Mutation: L19M, L25M Source method: isolated from a genetically manipulated source Details: complexed with 2,7-DIAMINOMITOSENE, residue MC / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.21 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, MES buffer, beta-octylglucoside, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2000 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. obs: 18054 / % possible obs: 99.9 % / Redundancy: 3.64 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4 / Num. unique all: 1776 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 66770 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.301 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.5→10 Å / Cross valid method: FREE R / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.124 / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.136 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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