HEADER INTEGRASE/DNA 21-JAN-99 1B69 TITLE THE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*GP*TP*AP*GP*TP*AP*AP*AP*TP*TP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*TP*TP*AP*CP*TP*AP*CP*TP*C)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROTEIN (INTEGRASE); COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: N-TERMINAL DNA BINDING DOMAIN; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 11 ORGANISM_TAXID: 1351; SOURCE 12 STRAIN: BL21(DE3); SOURCE 13 CELLULAR_LOCATION: CYTOPLASM; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS INTEGRASE, DNA BINDING, TRANSPOSITION, COMPLEX, BETA-SHEET KEYWDS 2 RECOGNITION, INTEGRASE-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR R.T.CLUBB,J.M.WOJCIAK,K.M.CONNOLLY REVDAT 7 27-DEC-23 1B69 1 SEQADV REVDAT 6 16-OCT-19 1B69 1 SOURCE REMARK ATOM REVDAT 5 14-MAR-18 1B69 1 REMARK SEQADV REVDAT 4 24-FEB-09 1B69 1 VERSN REVDAT 3 01-APR-03 1B69 1 JRNL REVDAT 2 28-OCT-99 1B69 1 HELIX REVDAT 1 29-SEP-99 1B69 0 JRNL AUTH J.M.WOJCIAK,K.M.CONNOLLY,R.T.CLUBB JRNL TITL NMR STRUCTURE OF THE TN916 INTEGRASE-DNA COMPLEX. JRNL REF NAT.STRUCT.BIOL. V. 6 366 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10201406 JRNL DOI 10.1038/7603 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007237. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY ETC. REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.843 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THREE AND FOUR-DIMENSIONAL HETERONUCLEAR NMR EXPERIMENTS 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: B, C, A 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT C 125 C5 DT C 125 C7 0.036 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 DG B 101 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 102 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG B 103 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 104 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 105 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 106 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 107 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 108 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 109 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA B 110 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 111 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 112 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 113 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG C 114 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA C 115 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 116 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT C 117 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT C 118 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT C 119 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA C 120 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC C 121 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT C 122 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT C 122 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA C 123 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 124 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT C 125 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC C 126 O4' - C1' - N1 ANGL. DEV. = 2.4 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 ARG A 9 -108.02 -104.99 REMARK 500 THR A 15 162.79 -46.76 REMARK 500 SER A 18 -162.84 -176.07 REMARK 500 ARG A 20 -154.16 -84.65 REMARK 500 SER A 32 11.66 -66.56 REMARK 500 PRO A 36 151.92 -42.80 REMARK 500 ALA A 46 65.70 -69.42 REMARK 500 THR A 47 -31.56 -151.78 REMARK 500 ASP A 48 -164.11 -68.14 REMARK 500 LYS A 69 -94.59 -74.50 REMARK 500 ASP A 70 -44.59 -157.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TN9 RELATED DB: PDB REMARK 900 20 STRUCTURES DBREF 1B69 A 3 71 UNP P22886 TNR6_ENTFA 3 71 DBREF 1B69 B 101 113 PDB 1B69 1B69 101 113 DBREF 1B69 C 114 126 PDB 1B69 1B69 114 126 SEQADV 1B69 ALA A 57 UNP P22886 CYS 57 ENGINEERED MUTATION SEQRES 1 B 13 DG DA DG DT DA DG DT DA DA DA DT DT DC SEQRES 1 C 13 DG DA DA DT DT DT DA DC DT DA DC DT DC SEQRES 1 A 69 GLU LYS ARG ARG ASP ASN ARG GLY ARG ILE LEU LYS THR SEQRES 2 A 69 GLY GLU SER GLN ARG LYS ASP GLY ARG TYR LEU TYR LYS SEQRES 3 A 69 TYR ILE ASP SER PHE GLY GLU PRO GLN PHE VAL TYR SER SEQRES 4 A 69 TRP LYS LEU VAL ALA THR ASP ARG VAL PRO ALA GLY LYS SEQRES 5 A 69 ARG ASP ALA ILE SER LEU ARG GLU LYS ILE ALA GLU LEU SEQRES 6 A 69 GLN LYS ASP ILE HELIX 1 1 SER A 59 LYS A 69 1 11 SHEET 1 A 3 GLU A 17 GLN A 19 0 SHEET 2 A 3 TYR A 25 ILE A 30 0 SHEET 3 A 3 PRO A 36 SER A 41 0 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