PDB Short entry for 1L1M HEADER TRANSCRIPTION REGULATOR/DNA 19-FEB-02 1L1M TITLE SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN TITLE 2 COMPLEXED TO ITS NATURAL OPERATOR O1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP COMPND 3 *AP*AP*TP*TP*T)-3'; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: LAC OPERATOR O1; THIS IS THE WILD-TYPE OPERATOR COMPND 7 SEQUENCE OF THE LAC OPERON IN E. COLI.; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP COMPND 10 *AP*AP*TP*TP*C)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: LAC OPERATOR O1; THIS IS THE WILD-TYPE OPERATOR COMPND 14 SEQUENCE OF THE LAC OPERON IN E. COLI.; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: LACTOSE OPERON REPRESSOR; COMPND 17 CHAIN: A, B; COMPND 18 FRAGMENT: N-TERMINAL DNA-BINDING DOMAIN, RESIDUES 1-62; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 GENE: LACI; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: DH9; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PGP1-2,PET-HP62 KEYWDS TRANSCRIPTION REGULATION, LAC OPERON, LAC REPRESSOR, NATURAL LAC KEYWDS 2 OPERATOR, ASYMMETRIC DNA-BINDING, HTH, TRANSCRIPTION REGULATOR-DNA KEYWDS 3 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.G.KALODIMOS,A.M.J.J.BONVIN,R.K.SALINAS,R.WECHSELBERGER,R.BOELENS, AUTHOR 2 R.KAPTEIN REVDAT 4 27-OCT-21 1L1M 1 REMARK SEQADV REVDAT 3 24-FEB-09 1L1M 1 VERSN REVDAT 2 01-APR-03 1L1M 1 JRNL REVDAT 1 26-JUN-02 1L1M 0 JRNL AUTH C.G.KALODIMOS,A.M.BONVIN,R.K.SALINAS,R.WECHSELBERGER, JRNL AUTH 2 R.BOELENS,R.KAPTEIN JRNL TITL PLASTICITY IN PROTEIN-DNA RECOGNITION: LAC REPRESSOR JRNL TITL 2 INTERACTS WITH ITS NATURAL OPERATOR 01 THROUGH ALTERNATIVE JRNL TITL 3 CONFORMATIONS OF ITS DNA-BINDING DOMAIN. JRNL REF EMBO J. V. 21 2866 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12065400 JRNL DOI 10.1093/EMBOJ/CDF318 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.G.KALODIMOS,G.FOLKERS,R.BOELENS,R.KAPTEIN REMARK 1 TITL STRONG DNA BINDING BY COVALENTLY LINKED DIMERIC LAC REMARK 1 TITL 2 HEADPIECE: EVIDENCE FOR THE CRUCIAL ROLE OF THE HINGE REMARK 1 TITL 3 HELICES REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 98 6039 2001 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.101129898 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE OF THE COMPLEX WAS REMARK 3 CALCULATED AS FOLLOWS. FIRST THE STRUCTURE OF THE DIMERIC LAC REMARK 3 HP62-V52C WAS CALCULATED USING ONLY PROTEIN NMR RESTRAINTS. THE REMARK 3 50 BEST STRUCTURES WERE SELECTED AND DOCKED ONTO THE NATURAL LAC REMARK 3 OPERATOR B-DNA USING SIMULATED ANNEALING. DISTANCE AND PLANARITY REMARK 3 RESTRAINTS FOR THE DNA WERE INCORPORATED IN ORDER TO KEEP DNA REMARK 3 CLOSE TO B-DNA BUT ALLOWING A BEND NECESSARY TO ACCOMMODATE THE REMARK 3 TWO HEADPIECE MOLECULES ON THE DNA. REMARK 4 REMARK 4 1L1M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015560. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 315 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 10MM KPI, 20MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM LAC-HP62-V52C U-15N,13C, REMARK 210 10MM KPI, 20MM KCL, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.0, NMRVIEW 5.0.4, CNS REMARK 210 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING FOLLOWED BY REMARK 210 RESTRAINED MDR REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: REMARK 210 THIS STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D HOMO- AND REMARK 210 HETERONUCLEARNUCLEAR TECHNIQUES. REMARK 210 13C-15N LABELED PROTEIN WAS USED AND UNLABELED NUCLEOTIDE. REMARK 210 IN ADDITION ISOTOPE FILTER EXPERIMENTS WERE APPLIED TO OBTAIN REMARK 210 ADDITIONAL ASSIGNMENTS AND TO ASSIGN INTER-MOLECULAR NOES. FOR REMARK 210 FURTHER DETAILS SEE THE REFERENCE DESCRIBING THE STRUCTURES. 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: C, D, A, B 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 H21 DG C 10 O2 DC D 14 1.53 REMARK 500 H21 DG C 13 O2 DC D 11 1.58 REMARK 500 H61 DA C 19 O4 DT D 5 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 16 DG C 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES 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 VAL A 15 -166.54 -123.56 REMARK 500 1 GLN A 26 64.59 62.49 REMARK 500 1 ALA A 27 -84.22 -121.75 REMARK 500 1 ASN A 46 64.98 63.63 REMARK 500 1 LYS A 59 104.62 69.62 REMARK 500 1 ASN B 25 -73.26 -123.52 REMARK 500 1 PRO B 49 138.81 -38.67 REMARK 500 1 ASN B 50 97.13 -62.59 REMARK 500 1 LYS B 59 65.90 -153.77 REMARK 500 2 ALA A 27 -137.15 -95.15 REMARK 500 2 ASN A 46 63.02 68.34 REMARK 500 2 ASN B 25 -75.08 -98.20 REMARK 500 2 ALA B 27 95.20 -50.77 REMARK 500 2 SER B 31 41.26 -86.77 REMARK 500 2 ALA B 32 -61.45 67.84 REMARK 500 2 ASN B 46 65.73 67.36 REMARK 500 2 ASN B 50 95.73 -58.17 REMARK 500 2 LYS B 59 89.50 62.83 REMARK 500 3 VAL A 15 -166.15 -124.12 REMARK 500 3 ALA A 27 -141.58 -94.14 REMARK 500 3 ASN A 46 64.83 66.65 REMARK 500 3 LYS A 59 -138.83 39.81 REMARK 500 3 LYS B 2 70.56 62.09 REMARK 500 3 ASN B 25 -74.91 -64.29 REMARK 500 3 GLN B 26 16.33 -146.35 REMARK 500 3 TYR B 47 108.77 -59.27 REMARK 500 3 PRO B 49 119.13 -30.44 REMARK 500 3 ASN B 50 88.34 -67.19 REMARK 500 3 ALA B 57 -80.29 -69.64 REMARK 500 3 LYS B 59 120.81 70.40 REMARK 500 4 ALA A 27 30.17 -85.89 REMARK 500 4 SER A 28 -172.82 60.59 REMARK 500 4 ASN A 46 63.50 67.75 REMARK 500 4 ASN B 25 -72.18 -128.45 REMARK 500 4 PRO B 49 122.51 -28.21 REMARK 500 4 ALA B 57 44.12 -73.61 REMARK 500 4 SER B 61 41.04 -88.73 REMARK 500 5 ALA A 27 -148.58 -103.02 REMARK 500 5 ASN A 46 67.18 64.51 REMARK 500 5 GLN A 60 90.94 -66.60 REMARK 500 5 ASN B 25 -73.74 -72.55 REMARK 500 5 GLN B 26 41.06 -167.23 REMARK 500 5 ALA B 27 -117.15 64.61 REMARK 500 5 SER B 28 120.23 58.94 REMARK 500 5 TYR B 47 108.99 -52.66 REMARK 500 5 PRO B 49 130.49 -30.86 REMARK 500 5 LEU B 56 -70.60 -70.63 REMARK 500 6 LYS A 2 81.71 -159.93 REMARK 500 6 GLN A 26 -53.38 -129.10 REMARK 500 6 SER A 31 -89.14 -74.07 REMARK 500 REMARK 500 THIS ENTRY HAS 203 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1L1M A 1 62 UNP P03023 LACI_ECOLI 1 62 DBREF 1L1M B 1 62 UNP P03023 LACI_ECOLI 1 62 DBREF 1L1M C 1 23 PDB 1L1M 1L1M 1 23 DBREF 1L1M D 1 23 PDB 1L1M 1L1M 1 23 SEQADV 1L1M CYS A 52 UNP P03023 VAL 52 ENGINEERED MUTATION SEQADV 1L1M CYS B 52 UNP P03023 VAL 52 ENGINEERED MUTATION SEQRES 1 C 23 DG DA DA DT DT DG DT DG DA DG DC DG DG SEQRES 2 C 23 DA DT DA DA DC DA DA DT DT DT SEQRES 1 D 23 DA DA DA DT DT DG DT DT DA DT DC DC DG SEQRES 2 D 23 DC DT DC DA DC DA DA DT DT DC 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 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 SER A 31 LEU A 45 1 15 HELIX 4 4 ASN A 50 GLY A 58 1 9 HELIX 5 5 THR B 5 GLY B 14 1 10 HELIX 6 6 SER B 16 ASN B 25 1 10 HELIX 7 7 SER B 31 LEU B 45 1 15 HELIX 8 8 ASN B 50 GLY B 58 1 9 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