10 20 30 40 50 60 70 80 2KEJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION/DNA 30-JAN-09 2KEJ
TITLE SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING TITLE 2 DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOSE OPERON REPRESSOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-62; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*GP*AP*AP*AP*TP*GP*TP*GP*AP*GP*CP*GP*AP*GP*TP*AP*AP*CP*AP COMPND 10 *AP*CP*CP*G)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(P*CP*GP*GP*TP*TP*GP*TP*TP*AP*CP*TP*CP*GP*CP*TP*CP*AP*CP*A COMPND 16 P*TP*TP*TP*C)-3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: LACI, B0345, JW0336; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH9; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES
KEYWDS LAC REPRESSOR, LAC OPERATORS, NMR, PROTEIN-DNA COMPLEX, DNA- KEYWDS 2 BINDING, REPRESSOR, TRANSCRIPTION, TRANSCRIPTION KEYWDS 3 REGULATION, TRANSCRIPTION/DNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.ROMANUKA,G.FOLKERS,N.BIRIS,E.TISHCHENKO,H.WIENK,R.KAPTEIN, AUTHOR 2 R.BOELENS
REVDAT 3 07-JUL-09 2KEJ 1 JRNL REVDAT 2 16-JUN-09 2KEJ 1 ATOM REVDAT 1 19-MAY-09 2KEJ 0
JRNL AUTH J.ROMANUKA,G.E.FOLKERS,N.BIRIS,E.TISHCHENKO, JRNL AUTH 2 H.WIENK,A.M.BONVIN,R.KAPTEIN,R.BOELENS JRNL TITL SPECIFICITY AND AFFINITY OF LAC REPRESSOR FOR THE JRNL TITL 2 AUXILIARY OPERATORS O2 AND O3 ARE EXPLAINED BY THE JRNL TITL 3 STRUCTURES OF THEIR PROTEIN-DNA COMPLEXES. JRNL REF J.MOL.BIOL. V. 390 478 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19450607 JRNL DOI 10.1016/J.JMB.2009.05.022
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, HADDOCK 2.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), DOMINGUEZ, BOELENS, BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KEJ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-09. REMARK 100 THE RCSB ID CODE IS RCSB101022.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 315 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.03 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM DNA (5'-D(*DGP*DAP* REMARK 210 DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DGP*DAP*DTP*DAP*DAP* REMARK 210 DCP*DAP*DAP*DTP*DTP*DT)'), 0.7 MM DNA (5'-D(P*DAP*DAP*DAP*DTP* REMARK 210 DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP* REMARK 210 DAP*DTP*DTP*DC)'), 0.7 MM LAC HEADPIECE DIMER, 5% D2O, 10 MM REMARK 210 POTASSIUM PHOSPHATE, 20 MM POTASSIUM CHLORIDE, 5% U-100% 2H REMARK 210 D8-GLYCEROL, 0.01% SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N REMARK 210 NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 900 MHZ; REMARK 210 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 TYR A 17 -9.81 -48.38 REMARK 500 1 GLN A 26 -77.91 -124.30 REMARK 500 1 ALA A 27 31.65 104.11 REMARK 500 1 ALA A 57 10.49 -63.34 REMARK 500 1 LYS A 59 -88.52 -142.53 REMARK 500 1 PRO B 3 88.37 -67.60 REMARK 500 1 GLN B 26 51.28 38.18 REMARK 500 1 ALA B 27 -26.01 -163.05 REMARK 500 1 SER B 28 -168.75 -73.46 REMARK 500 1 ASN B 46 60.33 65.36 REMARK 500 2 GLN B 26 -57.25 156.75 REMARK 500 2 ALA B 27 172.31 172.07 REMARK 500 2 SER B 28 88.30 155.48 REMARK 500 3 SER A 16 -165.60 -74.71 REMARK 500 3 SER A 28 64.14 -116.82 REMARK 500 3 HIS A 29 49.55 -143.52 REMARK 500 3 SER A 61 73.60 -107.57 REMARK 500 3 VAL B 4 -143.59 -124.24 REMARK 500 3 SER B 28 -173.26 76.75 REMARK 500 3 ASN B 46 70.45 68.73 REMARK 500 3 ALA B 57 9.40 -62.73 REMARK 500 4 VAL A 15 176.22 -57.34 REMARK 500 4 TYR A 17 -18.86 -36.97 REMARK 500 4 GLN A 26 -78.12 -120.17 REMARK 500 4 ALA A 27 12.34 101.63 REMARK 500 4 ASN A 46 72.50 67.63 REMARK 500 4 LYS A 59 24.19 -144.59 REMARK 500 4 GLN A 60 99.84 -45.61 REMARK 500 4 ALA B 27 64.20 -161.83 REMARK 500 4 SER B 28 -91.16 -154.93 REMARK 500 4 HIS B 29 27.49 -150.79 REMARK 500 4 ASN B 46 61.78 60.52 REMARK 500 4 ALA B 57 6.32 -60.58 REMARK 500 5 SER A 16 -169.84 -77.37 REMARK 500 5 HIS A 29 52.64 -161.32 REMARK 500 5 GLN A 60 -107.13 -112.05 REMARK 500 5 GLN B 26 57.24 36.91 REMARK 500 5 SER B 28 -14.59 71.95 REMARK 500 5 HIS B 29 45.12 -93.82 REMARK 500 5 ASN B 46 62.04 68.26 REMARK 500 5 ASN B 50 99.02 -67.35 REMARK 500 6 HIS A 29 41.33 -154.51 REMARK 500 6 ALA A 57 12.52 -68.13 REMARK 500 6 LYS A 59 16.84 -148.99 REMARK 500 6 PRO B 3 92.06 -68.91 REMARK 500 6 VAL B 15 177.70 -52.38 REMARK 500 6 GLN B 26 -48.43 168.75 REMARK 500 6 ALA B 27 -66.77 -177.58 REMARK 500 6 HIS B 29 52.76 70.10 REMARK 500 7 LYS A 2 96.16 62.90 REMARK 500 7 HIS A 29 57.92 -160.51 REMARK 500 7 ASN A 46 71.87 62.86 REMARK 500 7 LYS A 59 -12.77 163.12 REMARK 500 7 GLN A 60 -12.19 88.92 REMARK 500 7 VAL B 4 -153.96 45.48 REMARK 500 7 VAL B 15 -159.07 -62.19 REMARK 500 7 SER B 16 -169.88 -116.39 REMARK 500 7 ASN B 46 66.59 63.89 REMARK 500 7 ASN B 50 84.31 59.72 REMARK 500 7 ALA B 57 13.37 -64.42 REMARK 500 7 SER B 61 53.82 -146.91 REMARK 500 8 VAL A 15 172.64 -43.46 REMARK 500 8 HIS A 29 45.77 -150.63 REMARK 500 8 ASN A 46 61.74 60.92 REMARK 500 8 LYS A 59 15.04 -141.18 REMARK 500 8 GLN A 60 115.69 -36.11 REMARK 500 8 LYS B 2 -50.41 -168.28 REMARK 500 8 PRO B 3 100.57 -56.62 REMARK 500 8 GLN B 26 -41.40 75.80 REMARK 500 8 ALA B 27 -156.43 -108.37 REMARK 500 8 SER B 28 72.00 55.42 REMARK 500 8 HIS B 29 64.99 60.66 REMARK 500 8 ASN B 46 75.42 68.18 REMARK 500 8 LYS B 59 -38.10 171.95 REMARK 500 8 GLN B 60 39.36 -149.33 REMARK 500 9 GLN A 26 54.96 83.56 REMARK 500 9 HIS A 29 49.72 -158.36 REMARK 500 9 ASN A 46 65.54 61.34 REMARK 500 9 ASN A 50 117.03 -39.97 REMARK 500 9 SER A 61 70.28 -104.73 REMARK 500 9 PRO B 3 -158.26 -86.87 REMARK 500 9 GLN B 26 -65.93 172.12 REMARK 500 9 ALA B 27 -81.03 -177.52 REMARK 500 9 SER B 28 93.25 53.19 REMARK 500 9 ASN B 46 69.07 62.89 REMARK 500 9 PRO B 49 85.77 -67.07 REMARK 500 9 ASN B 50 129.82 -32.58 REMARK 500 10 HIS A 29 65.69 70.00 REMARK 500 10 GLN A 60 -167.35 64.73 REMARK 500 10 TYR B 17 -14.61 -44.39 REMARK 500 10 ALA B 27 27.17 -169.73 REMARK 500 10 SER B 28 -89.70 -108.91 REMARK 500 10 ASN B 46 73.41 64.11 REMARK 500 11 SER A 16 -167.49 -79.26 REMARK 500 11 HIS A 29 41.65 -158.36 REMARK 500 11 ALA A 57 4.30 -65.57 REMARK 500 11 LYS A 59 -91.93 -149.33 REMARK 500 11 GLN A 60 81.39 66.00 REMARK 500 11 PRO B 3 94.24 -58.04 REMARK 500 11 SER B 28 91.29 48.70 REMARK 500 11 ASN B 46 68.50 65.35 REMARK 500 11 LYS B 59 -91.18 -150.80 REMARK 500 12 HIS A 29 49.48 -153.33 REMARK 500 12 PRO B 3 -159.00 -87.90 REMARK 500 12 GLN B 26 -57.29 177.77 REMARK 500 12 ALA B 27 -68.36 178.24 REMARK 500 12 SER B 28 83.39 36.93 REMARK 500 12 ASN B 46 63.17 61.10 REMARK 500 12 ALA B 57 7.41 -62.45 REMARK 500 13 LYS A 2 83.01 53.78 REMARK 500 13 VAL A 15 164.49 -43.89 REMARK 500 13 TYR A 17 -23.94 -38.25 REMARK 500 13 HIS A 29 61.69 -161.73 REMARK 500 13 ASN A 46 70.44 58.61 REMARK 500 13 GLN A 60 99.53 51.12 REMARK 500 13 VAL B 4 -154.06 49.76 REMARK 500 13 ASN B 46 70.88 71.51 REMARK 500 13 ASN B 50 78.69 65.10 REMARK 500 13 ALA B 57 11.61 -63.37 REMARK 500 14 GLN A 26 117.06 78.21 REMARK 500 14 ALA A 27 -162.98 -120.33 REMARK 500 14 ASN A 46 68.62 60.03 REMARK 500 14 ALA A 57 1.85 -67.93 REMARK 500 14 VAL B 15 -174.55 -56.59 REMARK 500 14 GLN B 26 52.56 32.77 REMARK 500 14 LYS B 59 43.87 -141.60 REMARK 500 14 GLN B 60 94.25 -42.71 REMARK 500 15 LYS B 2 98.45 -168.61 REMARK 500 15 PRO B 3 -73.35 -82.82 REMARK 500 15 GLN B 26 -58.40 176.11 REMARK 500 15 ALA B 27 -62.44 171.09 REMARK 500 15 SER B 28 75.95 42.80 REMARK 500 15 ASN B 46 65.94 67.30 REMARK 500 15 LYS B 59 47.59 -97.61 REMARK 500 16 HIS A 29 56.08 -161.20 REMARK 500 16 ALA A 57 9.42 -67.59 REMARK 500 16 LYS A 59 12.62 -141.04 REMARK 500 16 SER A 61 34.49 -85.14 REMARK 500 16 LYS B 2 70.80 -153.51 REMARK 500 16 PRO B 3 -151.93 -92.18 REMARK 500 16 GLN B 26 51.65 39.45 REMARK 500 16 SER B 28 -171.21 66.83 REMARK 500 16 ASN B 46 62.84 66.16 REMARK 500 17 HIS A 29 54.60 -151.65 REMARK 500 17 SER A 61 16.66 -146.86 REMARK 500 17 SER B 28 176.22 62.31 REMARK 500 17 ASN B 46 63.83 68.75 REMARK 500 17 ASN B 50 95.45 -68.66 REMARK 500 18 PRO A 3 47.51 -84.63 REMARK 500 18 SER A 16 -169.65 -75.33 REMARK 500 18 GLN A 26 -80.07 -124.69 REMARK 500 18 ALA A 27 12.11 100.16 REMARK 500 18 ALA B 27 48.61 -147.84 REMARK 500 18 SER B 28 -152.35 -154.13 REMARK 500 19 HIS A 29 41.20 -151.10 REMARK 500 19 ALA A 57 12.83 -66.12 REMARK 500 19 LYS A 59 -86.46 -150.15 REMARK 500 19 PRO B 3 90.99 -57.18 REMARK 500 19 VAL B 15 -177.42 -55.19 REMARK 500 19 ALA B 27 -171.39 179.54 REMARK 500 19 SER B 28 70.29 54.65 REMARK 500 19 HIS B 29 64.37 65.58 REMARK 500 19 ASN B 46 66.21 62.63 REMARK 500 20 PRO A 3 75.39 -65.97 REMARK 500 20 HIS A 29 50.47 -150.13 REMARK 500 20 ALA A 57 10.11 -64.76 REMARK 500 20 PRO B 3 -156.63 -83.90 REMARK 500 20 GLN B 26 57.21 38.02 REMARK 500 20 SER B 28 -30.37 70.79 REMARK 500 20 HIS B 29 45.18 -83.93 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1L1M RELATED DB: PDB REMARK 900 RELATED ID: 2KEI RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO ITS NATURAL OPERATOR O1 REMARK 900 RELATED ID: 2KEK RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO ITS NATURAL OPERATOR O3
DBREF 2KEJ A 1 62 UNP P03023 LACI_ECOLI 1 62 DBREF 2KEJ B 1 62 UNP P03023 LACI_ECOLI 1 62 DBREF 2KEJ C -1 22 PDB 2KEJ 2KEJ 1 23 DBREF 2KEJ D -1 22 PDB 2KEJ 2KEJ 1 23
SEQADV 2KEJ CYS A 52 UNP P03023 VAL 52 ENGINEERED SEQADV 2KEJ CYS B 52 UNP P03023 VAL 52 ENGINEERED
SEQRES 1 A 62 MET LYS PRO VAL THR LEU TYR ASP VAL ALA GLU TYR ALA SEQRES 2 A 62 GLY VAL SER TYR GLN THR VAL SER ARG VAL VAL ASN GLN SEQRES 3 A 62 ALA SER HIS VAL SER ALA LYS THR ARG GLU LYS VAL GLU SEQRES 4 A 62 ALA ALA MET ALA GLU LEU ASN TYR ILE PRO ASN ARG CYS SEQRES 5 A 62 ALA GLN GLN LEU ALA GLY LYS GLN SER LEU SEQRES 1 B 62 MET LYS PRO VAL THR LEU TYR ASP VAL ALA GLU TYR ALA SEQRES 2 B 62 GLY VAL SER TYR GLN THR VAL SER ARG VAL VAL ASN GLN SEQRES 3 B 62 ALA SER HIS VAL SER ALA LYS THR ARG GLU LYS VAL GLU SEQRES 4 B 62 ALA ALA MET ALA GLU LEU ASN TYR ILE PRO ASN ARG CYS SEQRES 5 B 62 ALA GLN GLN LEU ALA GLY LYS GLN SER LEU SEQRES 1 C 23 DG DA DA DA DT DG DT DG DA DG DC DG DA SEQRES 2 C 23 DG DT DA DA DC DA DA DC DC DG SEQRES 1 D 23 DC DG DG DT DT DG DT DT DA DC DT DC DG SEQRES 2 D 23 DC DT DC DA DC DA DT DT DT DC
HELIX 1 1 THR A 5 GLY A 14 1 10 HELIX 2 2 GLN A 18 GLN A 26 1 9 HELIX 3 3 SER A 31 LEU A 45 1 15 HELIX 4 4 ASN A 50 ALA A 57 1 8 HELIX 5 5 THR B 5 GLY B 14 1 10 HELIX 6 6 SER B 16 GLN B 26 1 11 HELIX 7 7 SER B 31 ASN B 46 1 16 HELIX 8 8 ASN B 50 ALA B 57 1 8
SSBOND 1 CYS A 52 CYS B 52 1555 1555 2.03
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000