HEADER DNA BINDING PROTEIN 06-SEP-11 2LJ6 TITLE SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF THE PHOSPHOESTERASE TITLE 2 DOMAIN OF DNA LIGASE D COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT DNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-177; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: PA2138; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET28B+ KEYWDS PHOSPHOESTERASE, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR K.DUTTA,A.NATARAJAN,S.SHUMAN,R.GHOSE REVDAT 3 14-JUN-23 2LJ6 1 REMARK REVDAT 2 28-MAR-12 2LJ6 1 JRNL REVDAT 1 16-NOV-11 2LJ6 0 JRNL AUTH A.NATARAJAN,K.DUTTA,D.B.TEMEL,P.A.NAIR,S.SHUMAN,R.GHOSE JRNL TITL SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF THE JRNL TITL 2 PHOSPHOESTERASE DOMAIN OF DNA LIGASE D. JRNL REF NUCLEIC ACIDS RES. V. 40 2076 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22084199 JRNL DOI 10.1093/NAR/GKR950 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, ARIA 2.3 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LJ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000102446. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 200 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 300 UM [U-100% 15N] PAE177, 10 % REMARK 210 D20, 90 % H20, 50 MM BIS-TRIS, REMARK 210 200 MM NACL, 5 MM DTT, 90% H2O/ REMARK 210 10% D2O; 300 UM [U-100% 13C; U- REMARK 210 100% 15N] PAE177, 10 % D20, 90 % REMARK 210 H20, 50 MM BIS-TRIS, 200 MM NACL, REMARK 210 5 MM DTT, 90% H2O/10% D2O; 300 REMARK 210 UM [U-13C; U-15N; U-2H] PAE177, REMARK 210 10 % D20, 90 % H20, 50 MM BIS- REMARK 210 TRIS, 200 MM NACL, 5 MM DTT, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HNCO; 3D TROSY; 3D HN(COCA)CB; REMARK 210 3D HN(CO)CA; 3D HNCACO; 3D CC(CO) REMARK 210 NH; 3D H(CCO)NH; 3D HBHA(CO)NH; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 8.1.27 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2048 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: ALL BACKBONE EXPERIMENTS WERE TROSY BASED 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-15 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 PRO A 6 REMARK 465 LEU A 7 REMARK 465 ALA A 8 REMARK 465 GLU A 9 REMARK 465 TYR A 10 REMARK 465 ALA A 11 REMARK 465 ARG A 12 REMARK 465 LYS A 13 REMARK 465 ARG A 14 REMARK 465 ASP A 15 REMARK 465 PHE A 16 REMARK 465 ARG A 17 REMARK 465 GLN A 18 REMARK 465 THR A 19 REMARK 465 PRO A 20 REMARK 465 GLU A 21 REMARK 465 PRO A 22 REMARK 465 SER A 23 REMARK 465 GLY A 24 REMARK 465 ARG A 25 REMARK 465 LYS A 26 REMARK 465 PRO A 27 REMARK 465 ARG A 28 REMARK 465 LYS A 29 REMARK 465 ASP A 30 REMARK 465 SER A 31 REMARK 465 THR A 32 REMARK 465 GLU A 164 REMARK 465 ALA A 165 REMARK 465 ARG A 166 REMARK 465 SER A 167 REMARK 465 LEU A 168 REMARK 465 ASP A 169 REMARK 465 ARG A 170 REMARK 465 PHE A 171 REMARK 465 ASP A 172 REMARK 465 VAL A 173 REMARK 465 LEU A 174 REMARK 465 LYS A 175 REMARK 465 GLU A 176 REMARK 465 ARG A 177 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 HG CYS A 69 OD2 ASP A 71 1.55 REMARK 500 O GLU A 121 H LYS A 125 1.57 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 A 34 -138.54 -82.24 REMARK 500 1 ALA A 44 -156.65 167.20 REMARK 500 1 ASP A 56 46.60 31.78 REMARK 500 1 VAL A 64 175.80 -59.85 REMARK 500 1 LEU A 70 -80.24 -75.39 REMARK 500 1 ASP A 71 160.82 69.30 REMARK 500 1 ALA A 73 -26.08 169.10 REMARK 500 1 VAL A 74 51.50 -115.62 REMARK 500 1 LYS A 75 119.44 -36.95 REMARK 500 1 ASP A 87 -27.53 74.85 REMARK 500 1 GLU A 92 -60.10 -92.88 REMARK 500 1 SER A 94 -161.30 64.95 REMARK 500 1 HIS A 99 -73.90 -60.20 REMARK 500 1 TYR A 100 23.87 -155.54 REMARK 500 1 ALA A 102 -63.94 -174.11 REMARK 500 1 ASP A 117 -144.46 -132.65 REMARK 500 1 LYS A 151 -78.58 -85.95 REMARK 500 1 GLN A 152 -48.68 -175.14 REMARK 500 1 LYS A 161 73.94 -112.66 REMARK 500 2 LEU A 34 -139.80 -81.52 REMARK 500 2 ASP A 43 96.72 75.83 REMARK 500 2 ALA A 44 -81.22 63.76 REMARK 500 2 SER A 45 -60.49 -145.50 REMARK 500 2 LEU A 47 -62.38 -100.83 REMARK 500 2 TYR A 49 -102.16 -165.32 REMARK 500 2 LYS A 66 78.00 -179.45 REMARK 500 2 LEU A 70 -79.99 -73.74 REMARK 500 2 ASP A 71 160.50 69.19 REMARK 500 2 ALA A 73 -27.84 174.77 REMARK 500 2 VAL A 74 57.87 -111.88 REMARK 500 2 LYS A 75 112.63 -39.49 REMARK 500 2 LEU A 77 99.30 -53.11 REMARK 500 2 ASP A 87 4.91 82.92 REMARK 500 2 TYR A 88 49.90 -88.73 REMARK 500 2 ASP A 90 -73.05 -100.12 REMARK 500 2 SER A 94 -110.34 78.58 REMARK 500 2 ALA A 102 -81.99 -169.37 REMARK 500 2 ASP A 117 -139.67 -117.46 REMARK 500 2 SER A 138 177.88 177.79 REMARK 500 2 ARG A 149 120.33 68.39 REMARK 500 2 LYS A 151 -82.80 -82.09 REMARK 500 2 GLN A 152 -43.35 179.54 REMARK 500 2 SER A 153 -7.53 -142.58 REMARK 500 3 LEU A 34 -137.79 -80.89 REMARK 500 3 ASP A 43 148.12 85.77 REMARK 500 3 TYR A 49 -89.85 -160.72 REMARK 500 3 LYS A 66 139.42 157.31 REMARK 500 3 LEU A 70 -117.26 -82.90 REMARK 500 3 ASP A 71 154.80 162.70 REMARK 500 3 LEU A 77 89.28 -68.21 REMARK 500 REMARK 500 THIS ENTRY HAS 321 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17283 RELATED DB: BMRB DBREF 2LJ6 A 1 177 UNP Q9I1X7 Q9I1X7_PSEAE 1 177 SEQRES 1 A 177 MET PRO SER SER LYS PRO LEU ALA GLU TYR ALA ARG LYS SEQRES 2 A 177 ARG ASP PHE ARG GLN THR PRO GLU PRO SER GLY ARG LYS SEQRES 3 A 177 PRO ARG LYS ASP SER THR GLY LEU LEU ARG TYR CYS VAL SEQRES 4 A 177 GLN LYS HIS ASP ALA SER ARG LEU HIS TYR ASP PHE ARG SEQRES 5 A 177 LEU GLU LEU ASP GLY THR LEU LYS SER TRP ALA VAL PRO SEQRES 6 A 177 LYS GLY PRO CYS LEU ASP PRO ALA VAL LYS ARG LEU ALA SEQRES 7 A 177 VAL GLN VAL GLU ASP HIS PRO LEU ASP TYR ALA ASP PHE SEQRES 8 A 177 GLU GLY SER ILE PRO GLN GLY HIS TYR GLY ALA GLY ASP SEQRES 9 A 177 VAL ILE VAL TRP ASP ARG GLY ALA TRP THR PRO LEU ASP SEQRES 10 A 177 ASP PRO ARG GLU GLY LEU GLU LYS GLY HIS LEU SER PHE SEQRES 11 A 177 ALA LEU ASP GLY GLU LYS LEU SER GLY ARG TRP HIS LEU SEQRES 12 A 177 ILE ARG THR ASN LEU ARG GLY LYS GLN SER GLN TRP PHE SEQRES 13 A 177 LEU VAL LYS ALA LYS ASP GLY GLU ALA ARG SER LEU ASP SEQRES 14 A 177 ARG PHE ASP VAL LEU LYS GLU ARG HELIX 1 1 ASP A 87 ALA A 89 5 3 HELIX 2 2 ASP A 118 GLY A 126 1 9 SHEET 1 A10 PHE A 91 ILE A 95 0 SHEET 2 A10 GLY A 103 PRO A 115 -1 O VAL A 105 N GLY A 93 SHEET 3 A10 HIS A 127 GLY A 134 -1 O ASP A 133 N ALA A 112 SHEET 4 A10 TRP A 141 ARG A 145 -1 O LEU A 143 N LEU A 128 SHEET 5 A10 TRP A 155 LYS A 159 -1 O VAL A 158 N HIS A 142 SHEET 6 A10 ARG A 76 HIS A 84 -1 N ARG A 76 O LEU A 157 SHEET 7 A10 THR A 58 ALA A 63 -1 N SER A 61 O VAL A 81 SHEET 8 A10 HIS A 48 LEU A 55 -1 N LEU A 55 O THR A 58 SHEET 9 A10 LEU A 35 HIS A 42 -1 N HIS A 42 O HIS A 48 SHEET 10 A10 GLY A 103 PRO A 115 -1 O GLY A 111 N TYR A 37 CISPEP 1 VAL A 64 PRO A 65 1 5.53 CISPEP 2 ASP A 71 PRO A 72 1 -0.43 CISPEP 3 VAL A 64 PRO A 65 2 7.29 CISPEP 4 ASP A 71 PRO A 72 2 0.42 CISPEP 5 VAL A 64 PRO A 65 3 12.27 CISPEP 6 ASP A 71 PRO A 72 3 -9.57 CISPEP 7 VAL A 64 PRO A 65 4 10.27 CISPEP 8 ASP A 71 PRO A 72 4 5.78 CISPEP 9 VAL A 64 PRO A 65 5 11.27 CISPEP 10 ASP A 71 PRO A 72 5 0.58 CISPEP 11 VAL A 64 PRO A 65 6 12.58 CISPEP 12 ASP A 71 PRO A 72 6 -1.00 CISPEP 13 VAL A 64 PRO A 65 7 15.35 CISPEP 14 ASP A 71 PRO A 72 7 -13.59 CISPEP 15 VAL A 64 PRO A 65 8 9.51 CISPEP 16 ASP A 71 PRO A 72 8 2.36 CISPEP 17 VAL A 64 PRO A 65 9 21.98 CISPEP 18 ASP A 71 PRO A 72 9 10.30 CISPEP 19 VAL A 64 PRO A 65 10 3.46 CISPEP 20 ASP A 71 PRO A 72 10 -0.69 CISPEP 21 VAL A 64 PRO A 65 11 11.24 CISPEP 22 ASP A 71 PRO A 72 11 7.31 CISPEP 23 VAL A 64 PRO A 65 12 14.75 CISPEP 24 ASP A 71 PRO A 72 12 2.55 CISPEP 25 VAL A 64 PRO A 65 13 10.00 CISPEP 26 ASP A 71 PRO A 72 13 1.63 CISPEP 27 VAL A 64 PRO A 65 14 19.27 CISPEP 28 ASP A 71 PRO A 72 14 -13.65 CISPEP 29 VAL A 64 PRO A 65 15 20.35 CISPEP 30 ASP A 71 PRO A 72 15 6.67 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