| PDB link: | Open PDB home Structure Explorer page for 2iu5 | ||||||||||||||
| Deposition Date: | 27-may-06 | ||||||||||||||
| Resolution: | 1 Å | ||||||||||||||
| Unit Cell: |
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| Molecule: | mol_id: 1; molecule: hth-type dhaklm operon transcriptional activator chain: a, b; synonym: dhas, yceg; engineered: yes; mutation: yes | ||||||||||||||
| Functional Class: | transcription | ||||||||||||||
| Chemical Formula: | 294(h2 o) | ||||||||||||||
| Species: | mol_id: 1; organism_scientific: lactococcus lactis subsp. lactis organism_taxid: 272623; expression_system: escherichia coli; expression_system_taxid: 469008; expression_system_strain: bl21(de3); expression_system_vector_type: plasmid; expression_system_plasmid: pet28; other_details: nestle | ||||||||||||||
| Latest Update: | 13-jul-11 2iu5 1 versn | ||||||||||||||
| Primary Literature: | s.christen,a.srinivas,p.bahler,a.zeller,d.pridmore, c.bieniossek,u.baumann,b.erni Regulation of the dha operon of lactococcus lactis: deviation from the rule followed by the tetr family. transcription regulators. J.biol.chem., Page 23129, 2006 ASTM Number: , Published in: , ISSN: 0021-9258 | ||||||||||||||
| Refinement Programs: | refinement. program : refmac 5.2.0005 authors : murshudov,vagin,dodson refinement target : maximum likelihood data used in refinement. resolution range high (angstroms) : 1.60 resolution range low (angstroms) : 40.00 data cutoff (sigma(f)) : null completeness for range (%) : 99.3 number of reflections : 45492 fit to data used in refinement. cross-validation method : throughout free r value test set selection : random r value (working + test set) : 0.197 r value (working set) : 0.195 free r value : 0.230 free r value test set size (%) : 4.200 free r value test set count : 2013 fit in the highest resolution bin. total number of bins used : 20 bin resolution range high (a) : 1.60 bin resolution range low (a) : 1.64 reflection in bin (working set) : 3352 bin completeness (working+test) (%) : null bin r value (working set) : 0.2100 bin free r value set count : 105 bin free r value : 0.2860 number of non-hydrogen atoms used in refinement. protein atoms : 3034 nucleic acid atoms : 0 heterogen atoms : 0 solvent atoms : 294 b values. b value type : likely residual from wilson plot (a**2) : null mean b value (overall, a**2) : 23.23 overall anisotropic b value. b11 (a**2) : -0.51000 b22 (a**2) : 0.90000 b33 (a**2) : -0.39000 b12 (a**2) : 0.00000 b13 (a**2) : 0.00000 b23 (a**2) : 0.00000 estimated overall coordinate error. esu based on r value (a): 0.10 esu based on free r value (a): 0.10 esu based on maximum likelihood (a): 0.06 esu for b values based on maximum likelihood (a**2): 2.50 correlation coefficients. correlation coefficient fo-fc : 0.953 correlation coefficient fo-fc free : 0.935 rms deviations from ideal values count rms we bond lengths refined atoms (a): 3100 ; 0.008 ; 0. bond lengths others (a): null ; null ; n bond angles refined atoms (degrees): 4183 ; 1.682 ; 1. bond angles others (degrees): null ; null ; n torsion angles, period 1 (degrees): 354 ; 5.751 ; 5. torsion angles, period 2 (degrees): 175 ;38.076 ;25. torsion angles, period 3 (degrees): 578 ;16.380 ;15. torsion angles, period 4 (degrees): 12 ;24.349 ;15. chiral-center restraints (a**3): 450 ; 0.107 ; 0. general planes refined atoms (a): 2354 ; 0.001 ; 0. general planes others (a): null ; null ; n non-bonded contacts refined atoms (a): 1572 ; 0.239 ; 0. non-bonded contacts others (a): null ; null ; n non-bonded torsion refined atoms (a): 2236 ; 0.329 ; 0. non-bonded torsion others (a): null ; null ; n h-bond (x...y) refined atoms (a): 192 ; 0.241 ; 0. h-bond (x...y) others (a): null ; null ; n potential metal-ion refined atoms (a): null ; null ; n potential metal-ion others (a): null ; null ; n symmetry vdw refined atoms (a): 68 ; 0.190 ; 0. symmetry vdw others (a): null ; null ; n symmetry h-bond refined atoms (a): 23 ; 0.229 ; 0. symmetry h-bond others (a): null ; null ; n symmetry metal-ion refined atoms (a): null ; null ; n symmetry metal-ion others (a): null ; null ; n isotropic thermal factor restraints. count rms we main-chain bond refined atoms (a**2): 1803 ; 1.313 ; 3. main-chain bond other atoms (a**2): null ; null ; n main-chain angle refined atoms (a**2): 2874 ; 1.901 ; 3. side-chain bond refined atoms (a**2): 1467 ; 2.601 ; 4. side-chain angle refined atoms (a**2): 1309 ; 4.032 ; 5. anisotropic thermal factor restraints. count rms wei rigid-bond restraints (a**2): null ; null ; n sphericity; free atoms (a**2): null ; null ; n sphericity; bonded atoms (a**2): null ; null ; n ncs restraints statistics number of different ncs groups : 1 ncs group number : 1 chain names : a b number of components ncs group : 1 component c ssseqi to c ssseqi code 1 a 4 a 179 3 1 b 4 b 179 3 group chain count rms weight tight positional 1 a (a): 704 ; 0.55 ; 0.05 loose positional 1 a (a): 796 ; 1.07 ; 5.00 tight thermal 1 a (a**2): 704 ; 1.52 ; 0.50 loose thermal 1 a (a**2): 796 ; 2.84 ; 10.00 tls details number of tls groups : 2 tls group : 1 number of components group : 1 components c ssseqi to c ssseqi residue range : a 4 a 179 origin for the group (a): 12.9390 34.0440 37.1100 t tensor t11: -0.1056 t22: -0.1496 t33: -0.1080 t12: 0.0061 t13: -0.0065 t23: -0.0045 l tensor l11: 1.2978 l22: 0.7674 l33: 1.3213 l12: 0.7990 l13: -1.0504 l23: -0.8178 s tensor s11: 0.0317 s12: 0.0371 s13: 0.0427 s21: -0.0078 s22: 0.0170 s23: 0.0360 s31: -0.0772 s32: 0.0145 s33: -0.0487 tls group : 2 number of components group : 1 components c ssseqi to c ssseqi residue range : b 4 b 179 origin for the group (a): 24.0200 29.2370 10.3320 t tensor t11: 0.0228 t22: 0.0201 t33: 0.0104 t12: 0.0080 t13: 0.0052 t23: -0.0046 l tensor l11: 0.8902 l22: 0.4763 l33: 1.4548 l12: 0.2113 l13: 0.4787 l23: 0.2751 s tensor s11: 0.0480 s12: -0.0020 s13: -0.0953 s21: -0.0387 s22: 0.0392 s23: -0.0232 s31: 0.0816 s32: 0.0512 s33: -0.0872 bulk solvent modelling. method used : babinet model with mask parameters for mask calculation vdw probe radius : 1.40 ion probe radius : 0.80 shrinkage radius : 0.80 other refinement remarks: hydrogens have been added in the riding positions. | ||||||||||||||
| Refinement Format: | 2iu5 complies with format v. 3.30, 13-jul-11 |