HEADER TRANSCRIPTION/DNA 30-JAN-09 2KEK TITLE SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN TITLE 2 COMPLEXED TO ITS NATURAL OPERATOR O3 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(*CP*GP*GP*CP*AP*GP*TP*GP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*AP*AP*TP*TP* COMPND 10 C)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(P*GP*AP*AP*TP*TP*GP*CP*GP*TP*TP*GP*CP*GP*CP*TP*CP*AP*CP*TP*GP*CP*CP COMPND 16 *G)-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, PROTEIN-DNA COMPLEX, DNA-BINDING, KEYWDS 2 REPRESSOR, TRANSCRIPTION, TRANSCRIPTION REGULATION, TRANSCRIPTION- KEYWDS 3 DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.ROMANUKA,G.FOLKERS,N.BIRIS,E.TISHCHENKO,H.WIENK,R.KAPTEIN,R.BOELENS REVDAT 5 20-NOV-24 2KEK 1 REMARK REVDAT 4 20-OCT-21 2KEK 1 REMARK DBREF SEQADV REVDAT 3 07-JUL-09 2KEK 1 JRNL REVDAT 2 16-JUN-09 2KEK 1 ATOM REVDAT 1 19-MAY-09 2KEK 0 JRNL AUTH J.ROMANUKA,G.E.FOLKERS,N.BIRIS,E.TISHCHENKO,H.WIENK, JRNL AUTH 2 A.M.BONVIN,R.KAPTEIN,R.BOELENS JRNL TITL SPECIFICITY AND AFFINITY OF LAC REPRESSOR FOR THE AUXILIARY JRNL TITL 2 OPERATORS O2 AND O3 ARE EXPLAINED BY THE STRUCTURES OF THEIR JRNL TITL 3 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 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 2KEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000101023. 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'-STRAND1-3'), 0.7 REMARK 210 MM DNA (5'-STRAND2-3'), 0.7 MM REMARK 210 LAC HEADPIECE DIMER, 5% D2O, 10 REMARK 210 MM POTASSIUM PHOSPHATE, 20 MM REMARK 210 POTASSIUM CHLORIDE, 5% U-100% 2H REMARK 210 D8-GLYCEROL, 0.01% SODIUM AZIDE, REMARK 210 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; 500 REMARK 210 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 : 10 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 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 DC C -1 H22 DG D 22 0.99 REMARK 500 H22 DG C 1 O2 DC D 21 1.50 REMARK 500 N3 DC C -1 H1 DG D 22 1.58 REMARK 500 OE1 GLU A 36 HZ1 LYS A 37 1.60 REMARK 500 O2 DC C -1 N2 DG D 22 1.97 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 5 -168.43 -110.42 REMARK 500 1 GLN A 26 -33.50 -134.02 REMARK 500 1 SER A 28 -134.97 -72.82 REMARK 500 1 SER A 31 -7.85 67.31 REMARK 500 1 ALA A 32 -27.96 75.12 REMARK 500 1 PRO A 49 50.64 -67.99 REMARK 500 1 ASN A 50 -160.15 54.76 REMARK 500 1 ARG A 51 -40.16 -145.13 REMARK 500 1 TYR B 17 -56.23 70.97 REMARK 500 1 ASN B 25 -63.89 -103.55 REMARK 500 1 GLN B 26 54.53 -167.40 REMARK 500 1 SER B 28 -85.33 -124.44 REMARK 500 1 ASN B 46 86.14 65.16 REMARK 500 1 CYS B 52 -69.84 -158.43 REMARK 500 2 PRO A 3 88.92 -62.97 REMARK 500 2 GLN A 26 -32.30 -160.22 REMARK 500 2 SER A 31 -23.67 65.19 REMARK 500 2 ALA A 32 -19.63 72.72 REMARK 500 2 ASN A 46 83.29 64.99 REMARK 500 2 PRO A 49 18.09 -63.99 REMARK 500 2 ASN A 50 165.06 60.09 REMARK 500 2 ALA A 53 -44.76 174.49 REMARK 500 2 VAL B 24 -74.05 -67.52 REMARK 500 2 ASN B 25 67.00 -155.33 REMARK 500 2 GLN B 26 -66.42 -139.39 REMARK 500 2 HIS B 29 41.49 -81.34 REMARK 500 2 PRO B 49 95.87 -43.98 REMARK 500 2 ALA B 53 -25.70 176.95 REMARK 500 2 LYS B 59 55.04 -91.74 REMARK 500 3 PRO A 3 46.81 -75.91 REMARK 500 3 THR A 5 -169.53 -126.50 REMARK 500 3 ASN A 25 -65.64 -94.68 REMARK 500 3 SER A 28 -155.08 -91.68 REMARK 500 3 HIS A 29 99.60 -66.64 REMARK 500 3 VAL A 30 69.76 -106.76 REMARK 500 3 SER A 31 -18.96 67.69 REMARK 500 3 PRO A 49 30.73 -66.98 REMARK 500 3 ASN A 50 -173.48 57.93 REMARK 500 3 ARG A 51 -42.97 -137.31 REMARK 500 3 LEU A 56 -7.11 -58.35 REMARK 500 3 LYS A 59 -139.49 63.91 REMARK 500 3 GLN A 60 -74.15 64.38 REMARK 500 3 LYS B 2 -52.32 -150.82 REMARK 500 3 TYR B 17 17.39 58.30 REMARK 500 3 ASN B 25 -76.67 -95.86 REMARK 500 3 SER B 28 -80.42 -142.07 REMARK 500 3 HIS B 29 57.50 -99.75 REMARK 500 3 PRO B 49 99.31 -50.68 REMARK 500 3 CYS B 52 -69.34 -176.30 REMARK 500 4 ASN A 25 -64.40 -90.91 REMARK 500 REMARK 500 THIS ENTRY HAS 160 RAMACHANDRAN OUTLIERS. 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: 2KEJ RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO ITS NATURAL OPERATOR O2 DBREF 2KEK A 1 62 UNP P03023 LACI_ECOLI 1 62 DBREF 2KEK B 1 62 UNP P03023 LACI_ECOLI 1 62 DBREF 2KEK C -1 22 PDB 2KEK 2KEK -1 22 DBREF 2KEK D -1 22 PDB 2KEK 2KEK -1 22 SEQADV 2KEK CYS A 52 UNP P03023 VAL 52 ENGINEERED MUTATION SEQADV 2KEK CYS B 52 UNP P03023 VAL 52 ENGINEERED MUTATION 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 DC DG DG DC DA DG DT DG DA DG DC DG DC SEQRES 2 C 23 DA DA DC DG DC DA DA DT DT DC SEQRES 1 D 23 DG DA DA DT DT DG DC DG DT DT DG DC DG SEQRES 2 D 23 DC DT DC DA DC DT DG DC DC DG HELIX 1 1 THR A 5 GLY A 14 1 10 HELIX 2 2 SER A 16 GLN A 26 1 11 HELIX 3 3 THR A 34 LEU A 45 1 12 HELIX 4 4 CYS A 52 ALA A 57 1 6 HELIX 5 5 THR B 5 GLY B 14 1 10 HELIX 6 6 TYR B 17 GLN B 26 1 10 HELIX 7 7 SER B 31 ASN B 46 1 16 HELIX 8 8 CYS B 52 LYS B 59 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 MODEL 1