PDB Short entry for 2C06 HEADER TOXIN 25-AUG-05 2C06 TITLE NMR-BASED MODEL OF THE COMPLEX OF THE TOXIN KID AND A 5-NUCLEOTIDE TITLE 2 SUBSTRATE RNA FRAGMENT (AUACA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: KID TOXIN PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN PEMK; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*AP*UP*AP*CP*AP)-3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: R1; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS DOCKING, DNA REPLICATION, MAZF, PLASMID MAINTENANCE, POST KEYWDS 2 SEGREGATIONAL KILLING, PROTEIN-RNA COMPLEX, RIBONUCLEASE, RNA KEYWDS 3 CLEAVAGE, RNASE, TOXIN-ANTITOXIN, TOXIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.B.KAMPHUIS,A.M.J.J.BONVIN,M.C.MONTI,M.LEMONNIER,A.MUNOZ-GOMEZ, AUTHOR 2 R.H.H.VAN DEN HEUVEL,R.DIAZ-OREJAS,R.BOELENS REVDAT 6 14-JUN-23 2C06 1 REMARK REVDAT 5 15-JAN-20 2C06 1 REMARK REVDAT 4 24-FEB-09 2C06 1 VERSN REVDAT 3 15-MAR-06 2C06 1 JRNL REVDAT 2 23-FEB-06 2C06 1 HELIX SHEET REVDAT 1 08-FEB-06 2C06 0 JRNL AUTH M.B.KAMPHUIS,A.M.J.J.BONVIN,M.C.MONTI,M.LEMONNIER, JRNL AUTH 2 A.MUNOZ-GOMEZ,R.H.H.VAN DEN HEUVEL,R.DIAZ-OREJAS,R.BOELENS JRNL TITL MODEL FOR RNA BINDING AND THE CATALYTIC SITE OF THE RNASE JRNL TITL 2 KID OF THE BACTERIAL PARD TOXIN-ANTITOXIN SYSTEM. JRNL REF J.MOL.BIOL. V. 357 115 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16413033 JRNL DOI 10.1016/J.JMB.2005.12.033 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE OF THE COMPLEX WAS CALCULATED REMARK 3 WITH HADDOCK FOLLOWING STANDARD PROTOCOLS DOMINGUEZ, BOELENS AND REMARK 3 BONVIN, JACS 2003, 125, 1731-1737 REMARK 4 REMARK 4 2C06 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1290025350. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.0 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 95% D2O / 5% WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, CNS, HADDOCK REMARK 210 METHOD USED : HADDOCK REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST 10 ENERGY STRUCTURES IN REMARK 210 LOWEST ENERGY CLUSTER REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE OF THE COMPLEX WAS DETERMINED WITH HADDOCK REMARK 210 USING 28 AMBIGUOUS INTERACTION RESTRAINTS DERIVED FROM NMR REMARK 210 CHEMICAL SHIFT PERTURBATION DATA, MUTAGENESIS DATA AND KNOWN RNA REMARK 210 CLEAVAGE MECHANISM, USING THE CRYSTAL STRUCTURE OF THE KID DIMER REMARK 210 (PDB ENTRY 1M1F) AS STARTING POINT. THE CHEMICAL SHIFT REMARK 210 PERTURBATION DATA WERE OBTAINED BY ANALYSIS OF 1H-15N HSQC REMARK 210 SPECTRA RECORDED WITH INCREASING RNA CONCENTRATIONS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 400 REMARK 400 COMPOUND REMARK 400 RESPONSIBLE FOR THE STABLE MAINTENANCE OF THE PLASMID REMARK 400 DURING CELL DIVISION 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 C THR A 110 N MET B 1 1.33 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 HIS A 17 45.13 -160.44 REMARK 500 1 THR A 46 -158.06 -133.61 REMARK 500 1 LEU A 61 -52.92 -136.49 REMARK 500 1 GLN A 76 74.58 -117.30 REMARK 500 1 ARG A 78 146.11 -170.24 REMARK 500 1 LEU A 90 -73.36 -105.25 REMARK 500 1 LEU A 102 1.05 -68.54 REMARK 500 1 ARG B 3 120.71 73.42 REMARK 500 1 PHE B 33 -40.53 -135.14 REMARK 500 1 THR B 68 94.75 -67.77 REMARK 500 1 CYS B 74 45.93 -79.81 REMARK 500 1 ASP B 75 -32.91 -135.60 REMARK 500 1 ILE B 80 -164.14 -126.96 REMARK 500 1 LYS B 83 -42.50 -137.65 REMARK 500 2 ALA A 55 74.02 -155.53 REMARK 500 2 PHE A 57 42.44 -82.26 REMARK 500 2 ARG B 3 113.72 71.95 REMARK 500 2 VAL B 36 -71.24 -82.39 REMARK 500 2 ALA B 52 -71.84 -130.93 REMARK 500 2 ARG B 53 106.97 -168.25 REMARK 500 2 ALA B 55 -155.15 -158.13 REMARK 500 2 LEU B 90 -69.52 -100.29 REMARK 500 3 ARG A 38 -2.80 71.69 REMARK 500 3 THR A 46 -115.78 -120.38 REMARK 500 3 ASN A 50 -50.42 -163.65 REMARK 500 3 ARG A 53 -169.29 -123.07 REMARK 500 3 ARG A 78 118.02 -166.70 REMARK 500 3 ARG B 3 123.73 78.82 REMARK 500 3 HIS B 17 31.34 -99.23 REMARK 500 3 GLU B 18 -167.70 -73.38 REMARK 500 3 VAL B 36 -65.39 -99.05 REMARK 500 4 ARG A 38 -1.09 74.04 REMARK 500 4 THR A 46 -160.44 -115.90 REMARK 500 4 THR A 68 107.80 -52.74 REMARK 500 4 LEU A 90 -89.04 -101.56 REMARK 500 4 ARG B 3 80.19 60.69 REMARK 500 4 GLN B 20 -167.37 -129.55 REMARK 500 4 ASN B 50 -78.70 -78.03 REMARK 500 4 CYS B 74 22.97 -71.17 REMARK 500 4 LEU B 109 47.50 -94.07 REMARK 500 5 ARG A 38 -10.74 73.96 REMARK 500 5 SER A 47 -85.02 -79.21 REMARK 500 5 PHE A 51 45.53 -91.05 REMARK 500 5 THR A 68 -164.10 -77.04 REMARK 500 5 LEU A 90 -71.84 -86.14 REMARK 500 5 ARG B 3 58.71 81.76 REMARK 500 5 ALA B 32 0.84 -69.01 REMARK 500 5 ARG B 38 -38.10 75.16 REMARK 500 5 THR B 68 97.47 -68.12 REMARK 500 5 LYS B 83 -55.93 -121.14 REMARK 500 REMARK 500 THIS ENTRY HAS 87 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M1F RELATED DB: PDB REMARK 900 KID TOXIN PROTEIN FROM E.COLI PLASMID R1 REMARK 900 RELATED ID: 6925 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DATABASE REFERENCE SEQUENCE FOR PEMK PROTEIN (UNIPROT REMARK 999 ACCESSION NUMBER P13976) IS THE CLOSEST MATCH TO KID TOXIN REMARK 999 PROTEIN. THEIR SEQUENCES ARE IDENTICAL, HOWEVER PEMK HAS REMARK 999 A LONG LEADER SEQUENCE NOT PRESENT IN KID TOXIN PROTEIN. DBREF 2C06 A 1 110 UNP P13976 PEMK_ECOLI 24 133 DBREF 2C06 B 1 110 UNP P13976 PEMK_ECOLI 24 133 DBREF 2C06 C 1 5 PDB 2C06 2C06 1 5 SEQRES 1 A 110 MET GLU ARG GLY GLU ILE TRP LEU VAL SER LEU ASP PRO SEQRES 2 A 110 THR ALA GLY HIS GLU GLN GLN GLY THR ARG PRO VAL LEU SEQRES 3 A 110 ILE VAL THR PRO ALA ALA PHE ASN ARG VAL THR ARG LEU SEQRES 4 A 110 PRO VAL VAL VAL PRO VAL THR SER GLY GLY ASN PHE ALA SEQRES 5 A 110 ARG THR ALA GLY PHE ALA VAL SER LEU ASP GLY VAL GLY SEQRES 6 A 110 ILE ARG THR THR GLY VAL VAL ARG CYS ASP GLN PRO ARG SEQRES 7 A 110 THR ILE ASP MET LYS ALA ARG GLY GLY LYS ARG LEU GLU SEQRES 8 A 110 ARG VAL PRO GLU THR ILE MET ASN GLU VAL LEU GLY ARG SEQRES 9 A 110 LEU SER THR ILE LEU THR SEQRES 1 B 110 MET GLU ARG GLY GLU ILE TRP LEU VAL SER LEU ASP PRO SEQRES 2 B 110 THR ALA GLY HIS GLU GLN GLN GLY THR ARG PRO VAL LEU SEQRES 3 B 110 ILE VAL THR PRO ALA ALA PHE ASN ARG VAL THR ARG LEU SEQRES 4 B 110 PRO VAL VAL VAL PRO VAL THR SER GLY GLY ASN PHE ALA SEQRES 5 B 110 ARG THR ALA GLY PHE ALA VAL SER LEU ASP GLY VAL GLY SEQRES 6 B 110 ILE ARG THR THR GLY VAL VAL ARG CYS ASP GLN PRO ARG SEQRES 7 B 110 THR ILE ASP MET LYS ALA ARG GLY GLY LYS ARG LEU GLU SEQRES 8 B 110 ARG VAL PRO GLU THR ILE MET ASN GLU VAL LEU GLY ARG SEQRES 9 B 110 LEU SER THR ILE LEU THR SEQRES 1 C 5 A U A C A HELIX 1 1 PRO A 30 ARG A 38 1 9 HELIX 2 2 ASP A 81 GLY A 86 1 6 HELIX 3 3 PRO A 94 THR A 107 1 14 HELIX 4 4 PRO B 30 ARG B 38 1 9 HELIX 5 5 PRO B 94 THR B 107 1 14 HELIX 6 6 ILE B 108 THR B 110 5 3 SHEET 1 A 6 LYS A 88 ARG A 92 0 SHEET 2 A 6 GLU A 5 SER A 10 -1 N ILE A 6 O LEU A 90 SHEET 3 A 6 THR A 22 ILE A 27 -1 O VAL A 25 N TRP A 7 SHEET 4 A 6 VAL A 41 THR A 46 -1 O VAL A 43 N LEU A 26 SHEET 5 A 6 VAL A 71 ARG A 73 -1 O VAL A 71 N THR A 46 SHEET 6 A 6 ALA A 58 SER A 60 -1 N VAL A 59 O VAL A 72 SHEET 1 B 5 LYS A 88 ARG A 92 0 SHEET 2 B 5 GLU A 5 SER A 10 -1 N ILE A 6 O LEU A 90 SHEET 3 B 5 THR A 22 ILE A 27 -1 O VAL A 25 N TRP A 7 SHEET 4 B 5 VAL A 41 THR A 46 -1 O VAL A 43 N LEU A 26 SHEET 5 B 5 ARG A 78 THR A 79 -1 O ARG A 78 N VAL A 42 SHEET 1 C 6 LYS B 88 ARG B 92 0 SHEET 2 C 6 GLU B 5 SER B 10 -1 N ILE B 6 O LEU B 90 SHEET 3 C 6 THR B 22 ILE B 27 -1 O VAL B 25 N TRP B 7 SHEET 4 C 6 VAL B 41 THR B 46 -1 O VAL B 43 N LEU B 26 SHEET 5 C 6 VAL B 71 ARG B 73 -1 O VAL B 71 N THR B 46 SHEET 6 C 6 ALA B 58 SER B 60 -1 N VAL B 59 O VAL B 72 SHEET 1 D 5 LYS B 88 ARG B 92 0 SHEET 2 D 5 GLU B 5 SER B 10 -1 N ILE B 6 O LEU B 90 SHEET 3 D 5 THR B 22 ILE B 27 -1 O VAL B 25 N TRP B 7 SHEET 4 D 5 VAL B 41 THR B 46 -1 O VAL B 43 N LEU B 26 SHEET 5 D 5 ARG B 78 THR B 79 -1 O ARG B 78 N VAL B 42 CISPEP 1 ASP A 12 PRO A 13 1 0.41 CISPEP 2 ASP B 12 PRO B 13 1 -0.35 CISPEP 3 ASP A 12 PRO A 13 2 0.16 CISPEP 4 ASP B 12 PRO B 13 2 -0.24 CISPEP 5 ASP A 12 PRO A 13 3 -0.11 CISPEP 6 ASP B 12 PRO B 13 3 0.10 CISPEP 7 ASP A 12 PRO A 13 4 0.15 CISPEP 8 ASP B 12 PRO B 13 4 -0.75 CISPEP 9 ASP A 12 PRO A 13 5 0.25 CISPEP 10 ASP B 12 PRO B 13 5 0.83 CISPEP 11 ASP A 12 PRO A 13 6 0.42 CISPEP 12 ASP B 12 PRO B 13 6 0.08 CISPEP 13 ASP A 12 PRO A 13 7 -0.01 CISPEP 14 ASP B 12 PRO B 13 7 0.80 CISPEP 15 ASP A 12 PRO A 13 8 -0.07 CISPEP 16 ASP B 12 PRO B 13 8 0.74 CISPEP 17 ASP A 12 PRO A 13 9 -0.08 CISPEP 18 ASP B 12 PRO B 13 9 0.31 CISPEP 19 ASP A 12 PRO A 13 10 0.42 CISPEP 20 ASP B 12 PRO B 13 10 0.68 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 2 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