HEADER TRANSCRIPTION/DNA 07-JAN-02 1KQQ TITLE SOLUTION STRUCTURE OF THE DEAD RINGER ARID-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DEAD RINGER PROTEIN; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: A/T RICH INTERACTION DOMAIN; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 7 ORGANISM_COMMON: FRUIT FLY; SOURCE 8 ORGANISM_TAXID: 7227; SOURCE 9 GENE: DRI; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS ARID, PROTEIN-DNA COMPLEX, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.IWAHARA,M.IWAHARA,G.W.DAUGHDRILL,J.FORD,R.T.CLUBB REVDAT 4 22-MAY-24 1KQQ 1 REMARK REVDAT 3 27-OCT-21 1KQQ 1 REMARK SEQADV REVDAT 2 24-FEB-09 1KQQ 1 VERSN REVDAT 1 06-MAR-02 1KQQ 0 JRNL AUTH J.IWAHARA,M.IWAHARA,G.W.DAUGHDRILL,J.FORD,R.T.CLUBB JRNL TITL THE STRUCTURE OF THE DEAD RINGER-DNA COMPLEX REVEALS HOW JRNL TITL 2 AT-RICH INTERACTION DOMAINS (ARIDS) RECOGNIZE DNA. JRNL REF EMBO J. V. 21 1197 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 11867548 JRNL DOI 10.1093/EMBOJ/21.5.1197 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.851 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 3402 RESTRAINTS REMARK 4 REMARK 4 1KQQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015241. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0MM DEAD RINGER-DNA COMPLEX REMARK 210 (PROTEIN U-13C,15N, DNA NA) 20MM REMARK 210 TRIS U-2H, 0.01% NAN3 NA, 0.5MM REMARK 210 EDTA NA, 5MM DTT U-2H; 1.4MM REMARK 210 DEAD RINGER-DNA COMPLEX (PROTEIN REMARK 210 U-13C,15N, DNA NA) 20MM TRIS U- REMARK 210 2H, 0.01% NAN3 NA, 0.5MM EDTA NA, REMARK 210 5MM DTT U-2H REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA; 2D_F1F2_13C-FILTERED_NOESY; 3D_F1_13C15N- REMARK 210 FILTERED_F2_13C-EDITED_NOESY; 3D_F1_13C15N-FILTERED_F2_15N- REMARK 210 EDITED_NOESY; 2D_F2_13C-FILTERED_NOESY; 2D_F1_13C-FILTERED_JUNSY; REMARK 210 3D HNHB REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.0, NMRVIEW 4.3, X-PLOR REMARK 210 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: REMARK 210 THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR METHODS REMARK 210 ALONG WITH VARIOUS ISOTOPE-FILTERED TECHNIQUES. RESIDUES 1-2 REMARK 210 AND 134-139 ARE DISORDERED IN SOLUTION. 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 ARG A 134 REMARK 465 ARG A 135 REMARK 465 SER A 136 REMARK 465 SER A 137 REMARK 465 TYR A 138 REMARK 465 GLY A 139 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 SER A 117 H THR A 118 1.25 REMARK 500 O ASP A 31 H PHE A 35 1.43 REMARK 500 O TRP A 78 H ILE A 82 1.48 REMARK 500 O MET A 49 HG SER A 52 1.48 REMARK 500 O PHE A 28 H LEU A 32 1.48 REMARK 500 O PRO A 119 H GLN A 123 1.49 REMARK 500 OD1 ASP A 22 H ARG A 25 1.52 REMARK 500 H MET A 49 O SER A 52 1.53 REMARK 500 O PRO A 108 H GLU A 112 1.57 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 C 421 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 9 DT B 407 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 11 DT C 421 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 12 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 13 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 14 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 15 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 16 DT B 407 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 16 DT B 408 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 17 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 18 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 19 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 20 DT C 421 C6 - C5 - C7 ANGL. DEV. = -3.8 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 ASP A 55 90.33 -66.31 REMARK 500 1 SER A 93 34.64 -96.05 REMARK 500 2 ILE A 19 -38.66 -37.56 REMARK 500 2 ASP A 55 92.38 -63.05 REMARK 500 2 SER A 89 0.61 -55.94 REMARK 500 2 SER A 93 35.02 -95.33 REMARK 500 3 ASP A 55 105.28 -56.41 REMARK 500 3 SER A 89 0.66 -58.19 REMARK 500 3 SER A 93 47.77 -102.46 REMARK 500 3 ARG A 131 171.34 -56.63 REMARK 500 3 GLU A 132 -156.59 -110.74 REMARK 500 4 ILE A 19 -39.26 -35.28 REMARK 500 4 ASP A 55 89.43 -65.17 REMARK 500 4 SER A 89 -1.24 -55.61 REMARK 500 4 SER A 93 43.37 -104.25 REMARK 500 5 TRP A 4 90.61 -37.86 REMARK 500 5 ILE A 19 -39.55 -37.79 REMARK 500 5 ALA A 50 37.98 73.15 REMARK 500 5 ASP A 55 88.51 -62.89 REMARK 500 5 TYR A 60 -73.66 -56.36 REMARK 500 5 SER A 89 -0.35 -57.57 REMARK 500 5 SER A 93 41.77 -101.88 REMARK 500 6 ASP A 55 88.59 -63.73 REMARK 500 6 SER A 89 1.16 -61.37 REMARK 500 6 SER A 93 34.29 -95.49 REMARK 500 7 ARG A 45 123.20 -176.45 REMARK 500 7 ASP A 55 91.57 -61.86 REMARK 500 7 SER A 89 -0.50 -56.38 REMARK 500 7 SER A 93 30.51 -92.04 REMARK 500 8 ASP A 55 93.26 -62.27 REMARK 500 8 TYR A 60 -70.64 -61.28 REMARK 500 8 SER A 89 0.01 -55.73 REMARK 500 8 SER A 93 40.07 -96.32 REMARK 500 9 TRP A 4 75.88 -114.23 REMARK 500 9 ASP A 55 99.96 -59.56 REMARK 500 9 GLU A 132 -153.60 -108.43 REMARK 500 10 TRP A 4 78.93 -113.90 REMARK 500 10 ILE A 19 -37.08 -38.02 REMARK 500 10 ARG A 45 120.23 -171.79 REMARK 500 10 ASP A 55 91.80 -63.05 REMARK 500 10 SER A 89 0.87 -63.44 REMARK 500 10 SER A 93 30.54 -90.50 REMARK 500 11 TRP A 4 91.19 -39.45 REMARK 500 11 ASN A 20 123.04 -178.04 REMARK 500 11 ASP A 55 89.60 -68.35 REMARK 500 11 SER A 89 -0.75 -55.83 REMARK 500 11 SER A 93 37.82 -94.20 REMARK 500 12 ASP A 55 90.68 -65.74 REMARK 500 12 SER A 89 1.42 -58.06 REMARK 500 12 SER A 93 30.95 -90.26 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1KQQ A 3 139 UNP Q24573 DRI_DROME 262 398 DBREF 1KQQ B 401 415 PDB 1KQQ 1KQQ 401 415 DBREF 1KQQ C 416 430 PDB 1KQQ 1KQQ 416 430 SEQADV 1KQQ GLY A 1 UNP Q24573 CLONING ARTIFACT SEQADV 1KQQ SER A 2 UNP Q24573 CLONING ARTIFACT SEQADV 1KQQ LEU A 96 UNP Q24573 PHE 355 ENGINEERED MUTATION SEQRES 1 B 15 DC DC DT DG DT DA DT DT DG DA DT DG DT SEQRES 2 B 15 DG DG SEQRES 1 C 15 DC DC DA DC DA DT DC DA DA DT DA DC DA SEQRES 2 C 15 DG DG SEQRES 1 A 139 GLY SER GLY TRP SER PHE GLU GLU GLN PHE LYS GLN VAL SEQRES 2 A 139 ARG GLN LEU TYR GLU ILE ASN ASP ASP PRO LYS ARG LYS SEQRES 3 A 139 GLU PHE LEU ASP ASP LEU PHE SER PHE MET GLN LYS ARG SEQRES 4 A 139 GLY THR PRO ILE ASN ARG LEU PRO ILE MET ALA LYS SER SEQRES 5 A 139 VAL LEU ASP LEU TYR GLU LEU TYR ASN LEU VAL ILE ALA SEQRES 6 A 139 ARG GLY GLY LEU VAL ASP VAL ILE ASN LYS LYS LEU TRP SEQRES 7 A 139 GLN GLU ILE ILE LYS GLY LEU HIS LEU PRO SER SER ILE SEQRES 8 A 139 THR SER ALA ALA LEU THR LEU ARG THR GLN TYR MET LYS SEQRES 9 A 139 TYR LEU TYR PRO TYR GLU CYS GLU LYS LYS ASN LEU SER SEQRES 10 A 139 THR PRO ALA GLU LEU GLN ALA ALA ILE ASP GLY ASN ARG SEQRES 11 A 139 ARG GLU GLY ARG ARG SER SER TYR GLY HELIX 1 1 PHE A 6 GLU A 18 1 13 HELIX 2 2 PRO A 23 ARG A 39 1 17 HELIX 3 3 LEU A 56 ALA A 65 1 10 HELIX 4 4 LEU A 69 LYS A 75 1 7 HELIX 5 5 TRP A 78 GLY A 84 1 7 HELIX 6 6 ALA A 94 TYR A 105 1 12 HELIX 7 7 TYR A 107 LYS A 113 1 7 HELIX 8 8 PRO A 119 ASN A 129 1 11 SHEET 1 A 2 ILE A 48 MET A 49 0 SHEET 2 A 2 SER A 52 VAL A 53 -1 N VAL A 53 O ILE A 48 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