HEADER PROTEIN/DNA 11-MAR-09 2WCC TITLE PHAGE LAMBDA INTDBD1-64 COMPLEX WITH P PRIME 2 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*DCP*DGP*DAP*DGP*DTP*DCP*DAP COMPND 3 *DAP*DAP*DAP*DTP*DC)-3'); COMPND 4 CHAIN: 1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: INTN(1-64) COMPLEX WITH 12 MER DOUBLE STRANDED P'2 COMPND 7 DNA; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*DGP*DAP*DTP*DTP*DTP*DTP*DGP COMPND 10 *DAP*DCP*DTP*DGP*DC)-3'); COMPND 11 CHAIN: 2; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: INTN(1-64) COMPLEX WITH 12 MER DOUBLE STRANDED P'2 COMPND 14 DNA; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: INTEGRASE; COMPND 17 CHAIN: 3; COMPND 18 FRAGMENT: P'2 DNA BINDING DOMAIN, RESIDUES 1-64; COMPND 19 SYNONYM: PHAGE LAMBDA INTN-DNA COMPLEX; COMPND 20 ENGINEERED: YES; COMPND 21 OTHER_DETAILS: INTN(1-64) COMPLEX WITH 12 MER DOUBLE STRANDED P'2 DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 4 ORGANISM_COMMON: PHAGE LAMBDA; SOURCE 5 ORGANISM_TAXID: 10710; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 9 ORGANISM_COMMON: PHAGE LAMBDA; SOURCE 10 ORGANISM_TAXID: 10710; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 13 ORGANISM_COMMON: PHAGE LAMBDA; SOURCE 14 ORGANISM_TAXID: 10710; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DNA INTEGRATION, DNA RECOMBINATION, EXCISION, INTEGRATION, PHAGE KEYWDS 2 LAMBDA, RECOMBINATION, PROTEIN DNA COMPLEX, PROTEIN/DNA, PROTEIN-DNA KEYWDS 3 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.A.FADEEV,M.D.SAM,R.T.CLUBB REVDAT 3 15-MAY-24 2WCC 1 REMARK REVDAT 2 12-MAY-09 2WCC 1 JRNL ATOM REVDAT 1 07-APR-09 2WCC 0 JRNL AUTH E.A.FADEEV,M.D.SAM,R.T.CLUBB JRNL TITL NMR STRUCTURE OF THE AMINO-TERMINAL DOMAIN OF THE LAMBDA JRNL TITL 2 INTEGRASE PROTEIN IN COMPLEX WITH DNA: IMMOBILIZATION OF A JRNL TITL 3 FLEXIBLE TAIL FACILITATES BETA- SHEET RECOGNITION OF THE JRNL TITL 4 MAJOR GROOVE. JRNL REF J.MOL.BIOL. V. 388 682 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19324050 JRNL DOI 10.1016/J.JMB.2009.03.041 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.14 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2WCC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290039018. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.15 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 40 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 7% D2O 93% WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N HSQC; 13 HSQC; 3D 15N NOESY; REMARK 210 3D 15N TOCSY; HNCO; HNCA; HNCACB; REMARK 210 CBCA(CO)NH; HNHB; HNHA; HNCACO; REMARK 210 HCCH COSY; HCCH TOCSY; 3D 13C REMARK 210 EDITED NOESY; 2D F1F2 13C REMARK 210 FILTERED NOESY; 2D F1 13C REMARK 210 FILTERED NOESY; 13C F1; F2 REMARK 210 FILTERED NOESY; 13C F1 FILTERED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : MARS, QUEEN, ATNOS CANDID REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 EXPERIMENTS ON 13C 15N LABELED PROTEIN, UNLABELED DNA. REMARK 210 INTERMOLECULAR NOES WERE MEASURED USING 13C FILTERED 2D NOESY , REMARK 210 13C-EDITED 3D NOESY AND 15N-EDITED 3D NOESY 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: 1, 2, 3 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 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 1 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 5 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 5 DT 2 17 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 7 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 11 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 12 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 14 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 DT 1 5 C6 - C5 - C7 ANGL. DEV. = -3.7 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 LEU 3 37 -75.69 -89.90 REMARK 500 1 HIS 3 59 -42.53 -156.70 REMARK 500 2 HIS 3 59 -167.13 -177.62 REMARK 500 2 HIS 3 61 47.34 -96.94 REMARK 500 3 LEU 3 37 40.85 -95.19 REMARK 500 3 LYS 3 62 51.11 -166.36 REMARK 500 4 LEU 3 37 -82.47 -89.64 REMARK 500 4 HIS 3 59 64.27 -164.81 REMARK 500 4 HIS 3 61 44.90 -96.45 REMARK 500 5 LEU 3 37 -78.93 -87.66 REMARK 500 5 HIS 3 61 -42.81 -135.52 REMARK 500 5 LYS 3 62 50.29 -160.72 REMARK 500 6 LEU 3 37 28.47 -145.09 REMARK 500 6 HIS 3 59 129.82 -170.40 REMARK 500 6 HIS 3 61 -43.17 -131.63 REMARK 500 7 LEU 3 37 32.75 -145.12 REMARK 500 7 HIS 3 61 -42.83 -132.14 REMARK 500 7 LYS 3 62 51.79 -162.44 REMARK 500 8 LEU 3 37 35.62 -97.17 REMARK 500 9 HIS 3 59 -145.97 -156.01 REMARK 500 10 ARG 3 3 107.78 -59.73 REMARK 500 10 SER 3 6 -167.54 -126.54 REMARK 500 10 THR 3 31 -32.63 -137.34 REMARK 500 10 LEU 3 37 33.74 -144.99 REMARK 500 12 LEU 3 37 24.94 -145.38 REMARK 500 12 HIS 3 59 -74.34 -157.06 REMARK 500 12 LYS 3 62 53.25 -171.80 REMARK 500 13 LEU 3 37 -70.70 -88.53 REMARK 500 13 HIS 3 59 -163.33 -164.64 REMARK 500 13 LYS 3 62 52.74 -169.58 REMARK 500 14 LEU 3 37 32.46 -92.47 REMARK 500 14 LYS 3 62 -52.92 173.20 REMARK 500 15 LEU 3 37 -73.88 -88.62 REMARK 500 15 HIS 3 59 -152.83 -168.88 REMARK 500 15 LYS 3 62 52.20 -170.06 REMARK 500 15 PRO 3 63 -178.65 -69.22 REMARK 500 16 ARG 3 3 108.43 -59.86 REMARK 500 16 LEU 3 37 32.88 -92.92 REMARK 500 16 HIS 3 59 -63.71 -166.72 REMARK 500 17 LEU 3 37 -74.31 -88.55 REMARK 500 17 HIS 3 61 -41.88 -135.48 REMARK 500 18 HIS 3 59 57.03 -175.01 REMARK 500 18 HIS 3 61 48.92 -107.65 REMARK 500 19 HIS 3 59 -178.26 -69.34 REMARK 500 19 LYS 3 62 50.99 -164.67 REMARK 500 20 LEU 3 37 -74.65 -88.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG 3 3 0.27 SIDE CHAIN REMARK 500 1 ARG 3 4 0.31 SIDE CHAIN REMARK 500 1 ARG 3 5 0.32 SIDE CHAIN REMARK 500 1 ARG 3 9 0.32 SIDE CHAIN REMARK 500 1 ARG 3 10 0.29 SIDE CHAIN REMARK 500 1 ARG 3 19 0.25 SIDE CHAIN REMARK 500 1 ARG 3 27 0.30 SIDE CHAIN REMARK 500 1 ARG 3 30 0.28 SIDE CHAIN REMARK 500 1 ARG 3 39 0.29 SIDE CHAIN REMARK 500 1 ARG 3 41 0.30 SIDE CHAIN REMARK 500 1 ARG 3 42 0.14 SIDE CHAIN REMARK 500 2 ARG 3 3 0.27 SIDE CHAIN REMARK 500 2 ARG 3 4 0.21 SIDE CHAIN REMARK 500 2 ARG 3 5 0.28 SIDE CHAIN REMARK 500 2 ARG 3 9 0.30 SIDE CHAIN REMARK 500 2 ARG 3 10 0.22 SIDE CHAIN REMARK 500 2 ARG 3 19 0.27 SIDE CHAIN REMARK 500 2 ARG 3 27 0.32 SIDE CHAIN REMARK 500 2 ARG 3 30 0.32 SIDE CHAIN REMARK 500 2 ARG 3 39 0.32 SIDE CHAIN REMARK 500 2 ARG 3 41 0.31 SIDE CHAIN REMARK 500 2 ARG 3 42 0.29 SIDE CHAIN REMARK 500 3 ARG 3 3 0.32 SIDE CHAIN REMARK 500 3 ARG 3 4 0.32 SIDE CHAIN REMARK 500 3 ARG 3 5 0.31 SIDE CHAIN REMARK 500 3 ARG 3 9 0.32 SIDE CHAIN REMARK 500 3 ARG 3 10 0.30 SIDE CHAIN REMARK 500 3 ARG 3 19 0.30 SIDE CHAIN REMARK 500 3 ARG 3 27 0.12 SIDE CHAIN REMARK 500 3 ARG 3 30 0.31 SIDE CHAIN REMARK 500 3 ARG 3 39 0.21 SIDE CHAIN REMARK 500 3 ARG 3 41 0.31 SIDE CHAIN REMARK 500 3 ARG 3 42 0.31 SIDE CHAIN REMARK 500 4 ARG 3 3 0.32 SIDE CHAIN REMARK 500 4 ARG 3 4 0.24 SIDE CHAIN REMARK 500 4 ARG 3 5 0.29 SIDE CHAIN REMARK 500 4 ARG 3 9 0.15 SIDE CHAIN REMARK 500 4 ARG 3 10 0.26 SIDE CHAIN REMARK 500 4 ARG 3 19 0.25 SIDE CHAIN REMARK 500 4 ARG 3 27 0.32 SIDE CHAIN REMARK 500 4 ARG 3 30 0.28 SIDE CHAIN REMARK 500 4 ARG 3 39 0.29 SIDE CHAIN REMARK 500 4 ARG 3 41 0.29 SIDE CHAIN REMARK 500 4 ARG 3 42 0.27 SIDE CHAIN REMARK 500 5 ARG 3 3 0.13 SIDE CHAIN REMARK 500 5 ARG 3 4 0.29 SIDE CHAIN REMARK 500 5 ARG 3 5 0.25 SIDE CHAIN REMARK 500 5 ARG 3 9 0.28 SIDE CHAIN REMARK 500 5 ARG 3 10 0.18 SIDE CHAIN REMARK 500 5 ARG 3 19 0.13 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 220 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z1G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A LAMBDA INTEGRASE TETRAMER BOUND TO AHOLLIDAY REMARK 900 JUNCTION REMARK 900 RELATED ID: 1Z1B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A LAMBDA INTEGRASE DIMER BOUND TO ACOC' CORE REMARK 900 SITE REMARK 900 RELATED ID: 1KJK RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE LAMBDA INTEGRASE AMINO-TERMINALDOMAIN REMARK 900 RELATED ID: 1Z19 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A LAMBDA INTEGRASE(75- 356) DIMER BOUNDTO A REMARK 900 COC' CORE SITE REMARK 900 RELATED ID: 1AE9 RELATED DB: PDB REMARK 900 STRUCTURE OF THE LAMBDA INTEGRASE CATALYTIC CORE REMARK 900 RELATED ID: 1M97 RELATED DB: PDB REMARK 900 CONSERVATION OF STRUCTURE AND FUNCTION AMONG TYROSINERECOMBINASES: REMARK 900 HOMOLOGY-BASED MODELING OF THE LAMBDAINTEGRASE CORE-BINDING DOMAIN REMARK 900 RELATED ID: 1P7D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LAMBDA INTEGRASE ( RESIDUES 75-356)BOUND REMARK 900 TO DNA DBREF 2WCC 1 1 12 PDB 2WCC 2WCC 1 12 DBREF 2WCC 2 13 24 PDB 2WCC 2WCC 13 24 DBREF 2WCC 3 1 64 UNP P03700 VINT_LAMBD 1 64 SEQRES 1 1 12 DG DC DA DG DT DC DA DA DA DA DT DC SEQRES 1 2 12 DG DA DT DT DT DT DG DA DC DT DG DC SEQRES 1 3 64 MET GLY ARG ARG ARG SER HIS GLU ARG ARG ASP LEU PRO SEQRES 2 3 64 PRO ASN LEU TYR ILE ARG ASN ASN GLY TYR TYR CYS TYR SEQRES 3 3 64 ARG ASP PRO ARG THR GLY LYS GLU PHE GLY LEU GLY ARG SEQRES 4 3 64 ASP ARG ARG ILE ALA ILE THR GLU ALA ILE GLN ALA ASN SEQRES 5 3 64 ILE GLU LEU PHE SER GLY HIS LYS HIS LYS PRO LEU HELIX 1 1 GLU 3 8 LEU 3 12 5 5 HELIX 2 2 ASP 3 40 PHE 3 56 1 17 SHEET 1 3A 3 LEU 3 16 ILE 3 18 0 SHEET 2 3A 3 TYR 3 24 ARG 3 27 -1 O CYS 3 25 N TYR 3 17 SHEET 3 3A 3 GLU 3 34 GLY 3 36 -1 O PHE 3 35 N TYR 3 26 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