Header list of 2c06.pdb file
Complete list - g 9 2 Bytes
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
MODEL 1
Complete list - g 9 2 Bytes