HEADER TRANSCRIPTION/DNA 29-DEC-06 2OEH TITLE DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE MRF2-DNA TITLE 2 COMPLEX USING PARAMAGNETIC SPIN LABELING COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*TP*AP*CP*AP*AP*TP*AP*TP*AP*AP*CP*GP*TP*CP*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*CP*GP*AP*CP*GP*TP*TP*AP*TP*AP*TP*TP*GP*T)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 5B; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: ARID DOMAIN; COMPND 13 SYNONYM: ARID DOMAIN- CONTAINING PROTEIN 5B, MRF1-LIKE, MODULATOR COMPND 14 RECOGNITION FACTOR 2, MRF-2; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SOLID PHASE SYNTHESIS; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: ARID5B, DESRT, MRF2; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MRF2, DNA, COMPLEX, SPIN LABELING, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR S.CAI,L.ZHU,Z.ZHANG REVDAT 4 27-DEC-23 2OEH 1 REMARK REVDAT 3 16-MAR-22 2OEH 1 REMARK REVDAT 2 24-FEB-09 2OEH 1 VERSN REVDAT 1 07-AUG-07 2OEH 0 JRNL AUTH S.CAI,L.ZHU,Z.ZHANG,Y.CHEN JRNL TITL DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE JRNL TITL 2 MRF2-DNA COMPLEX USING PARAMAGNETIC SPIN LABELING. JRNL REF BIOCHEMISTRY V. 46 4943 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17407261 JRNL DOI 10.1021/BI061738H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK, HADDOCK REMARK 3 AUTHORS : BONVIN, A. M. J. J. (HADDOCK), BONVIN, A. M. J. J. REMARK 3 (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 13 DISTANCE CONSTRAINTS FROM SPIN REMARK 3 LABELING; THE MAJORITY OF THE PROTEIN AND DNA ARE FIXED REMARK 4 REMARK 4 2OEH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041033. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM MRF-2 ARID DOMAIN, U-15N; REMARK 210 10MM PHOSPHATE BUFFER; 90% H2O, REMARK 210 10% D2O; PH=6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 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: NULL 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: 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 B 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 8 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 9 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 10 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 11 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 12 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 13 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 14 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 14 DA B 2 O3' - P - OP1 ANGL. DEV. = 8.6 DEGREES REMARK 500 15 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 17 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.1 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 ASN A 34 69.90 32.45 REMARK 500 1 SER A 72 29.31 -154.77 REMARK 500 1 ILE A 85 -21.77 -157.95 REMARK 500 1 GLU A 95 22.83 -142.13 REMARK 500 1 GLU A 96 -49.49 -151.83 REMARK 500 1 ASP A 97 145.32 -177.49 REMARK 500 1 LYS A 104 82.50 -168.12 REMARK 500 1 ARG A 106 -119.24 -162.92 REMARK 500 2 LYS A 31 -168.53 -127.09 REMARK 500 2 ASN A 34 79.31 38.49 REMARK 500 2 ILE A 85 -21.82 -157.97 REMARK 500 2 GLU A 95 22.89 -142.13 REMARK 500 2 GLU A 96 -49.83 -151.85 REMARK 500 2 ASP A 97 147.90 178.22 REMARK 500 2 LYS A 104 92.64 -176.61 REMARK 500 2 ARG A 106 -143.22 -161.34 REMARK 500 3 LYS A 31 -166.50 -120.18 REMARK 500 3 ASN A 34 80.20 36.26 REMARK 500 3 SER A 72 19.62 -164.52 REMARK 500 3 ILE A 85 -21.76 -157.96 REMARK 500 3 GLU A 95 22.84 -142.13 REMARK 500 3 GLU A 96 -49.67 -151.80 REMARK 500 3 LYS A 98 79.53 -156.33 REMARK 500 3 LYS A 104 67.01 -169.05 REMARK 500 4 GLN A 32 172.84 -59.67 REMARK 500 4 ASN A 34 83.80 25.43 REMARK 500 4 SER A 72 48.00 -103.43 REMARK 500 4 ILE A 85 -21.82 -157.96 REMARK 500 4 GLU A 95 22.92 -142.17 REMARK 500 4 GLU A 96 -48.76 -151.84 REMARK 500 4 LYS A 98 79.23 -150.37 REMARK 500 4 ARG A 106 -126.19 -130.31 REMARK 500 5 LYS A 31 -169.72 -122.88 REMARK 500 5 ASN A 34 75.33 39.47 REMARK 500 5 THR A 71 -2.96 -140.97 REMARK 500 5 SER A 72 39.97 -86.16 REMARK 500 5 ALA A 73 -25.73 -154.38 REMARK 500 5 ILE A 85 -21.82 -157.96 REMARK 500 5 GLU A 95 22.76 -142.10 REMARK 500 5 GLU A 96 -46.39 -151.74 REMARK 500 5 ASP A 97 -73.45 -89.25 REMARK 500 5 ARG A 106 -154.01 -107.37 REMARK 500 6 LYS A 31 -167.37 -122.31 REMARK 500 6 ASN A 34 79.21 35.56 REMARK 500 6 ILE A 85 -21.78 -157.97 REMARK 500 6 GLU A 95 22.88 -142.19 REMARK 500 6 GLU A 96 -49.56 -151.80 REMARK 500 7 LYS A 31 -169.53 -124.07 REMARK 500 7 ASN A 34 -154.51 49.78 REMARK 500 7 LEU A 35 -62.86 -174.08 REMARK 500 REMARK 500 THIS ENTRY HAS 126 RAMACHANDRAN OUTLIERS. 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 5 DT B 1 0.08 SIDE CHAIN REMARK 500 14 DT B 1 0.08 SIDE CHAIN REMARK 500 15 DT B 1 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 LEU A 64 13.76 REMARK 500 2 LEU A 64 14.64 REMARK 500 3 LEU A 64 13.81 REMARK 500 4 LEU A 64 14.14 REMARK 500 5 LEU A 64 12.83 REMARK 500 6 LEU A 64 13.65 REMARK 500 7 LEU A 64 15.40 REMARK 500 8 LEU A 64 13.24 REMARK 500 9 LEU A 64 13.85 REMARK 500 10 LEU A 64 12.00 REMARK 500 11 LEU A 64 14.85 REMARK 500 12 LEU A 64 14.85 REMARK 500 13 LEU A 64 13.63 REMARK 500 14 LEU A 64 14.80 REMARK 500 15 ILE A 25 10.33 REMARK 500 15 LEU A 64 14.33 REMARK 500 16 LEU A 64 12.33 REMARK 500 17 LEU A 64 10.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 2OEH A 1 107 UNP Q14865 ARI5B_HUMAN 318 424 DBREF 2OEH B 1 15 PDB 2OEH 2OEH 1 15 DBREF 2OEH C 16 29 PDB 2OEH 2OEH 16 29 SEQRES 1 B 15 DT DA DC DA DA DT DA DT DA DA DC DG DT SEQRES 2 B 15 DC DG SEQRES 1 C 14 DC DG DA DC DG DT DT DA DT DA DT DT DG SEQRES 2 C 14 DT SEQRES 1 A 107 ARG ALA ASP GLU GLN ALA PHE LEU VAL ALA LEU TYR LYS SEQRES 2 A 107 TYR MET LYS GLU ARG LYS THR PRO ILE GLU ARG ILE PRO SEQRES 3 A 107 TYR LEU GLY PHE LYS GLN ILE ASN LEU TRP THR MET PHE SEQRES 4 A 107 GLN ALA ALA GLN LYS LEU GLY GLY TYR GLU THR ILE THR SEQRES 5 A 107 ALA ARG ARG GLN TRP LYS HIS ILE TYR ASP GLU LEU GLY SEQRES 6 A 107 GLY ASN PRO GLY SER THR SER ALA ALA THR CYS THR ARG SEQRES 7 A 107 ARG HIS TYR GLU ARG LEU ILE LEU PRO TYR GLU ARG PHE SEQRES 8 A 107 ILE LYS GLY GLU GLU ASP LYS PRO LEU PRO PRO ILE LYS SEQRES 9 A 107 PRO ARG LYS HELIX 1 1 ARG A 1 GLU A 17 1 17 HELIX 2 2 PRO A 21 ILE A 25 5 5 HELIX 3 3 ASN A 34 LEU A 45 1 12 HELIX 4 4 GLY A 46 ARG A 55 1 10 HELIX 5 5 GLN A 56 GLY A 65 1 10 HELIX 6 6 CYS A 76 ILE A 85 1 10 HELIX 7 7 TYR A 88 GLU A 96 1 9 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