10 20 30 40 50 60 70 80 2OEH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION/DNA 29-DEC-06 2OEH
TITLE DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE TITLE 2 MRF2-DNA COMPLEX USING PARAMAGNETIC SPIN LABELING
COMPND MOL_ID: 1; COMPND 2 MOLECULE: AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ARID DOMAIN; COMPND 5 SYNONYM: ARID DOMAIN- CONTAINING PROTEIN 5B, MRF1-LIKE, COMPND 6 MODULATOR RECOGNITION FACTOR 2, MRF-2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'- COMPND 10 D(P*TP*AP*CP*AP*AP*TP*AP*TP*AP*AP*CP*GP*TP*CP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(P*CP*GP*AP*CP*GP*TP*TP*AP*TP*AP*TP*TP*GP*T)- COMPND 15 3'; COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ARID5B, DESRT, MRF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: SOLID PHASE SYNTHESIS; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SOLID PHASE SYNTHESIS
KEYWDS MRF2, DNA, COMPLEX, NMR, SPIN LABELING, TRANSCRIPTION/DNA KEYWDS 2 COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 17
AUTHOR S.CAI,L.ZHU,Z.ZHANG
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 JRNL TITL 2 OF THE MRF2-DNA COMPLEX USING PARAMAGNETIC SPIN JRNL TITL 3 LABELING. JRNL REF BIOCHEMISTRY V. 46 4943 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17407261 JRNL DOI 10.1021/BI061738H
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN, A. M. J. J. 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 RCSB ID CODE IS RCSB041033.
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- REMARK 210 15N; 10MM PHOSPHATE BUFFER; REMARK 210 90% H2O, 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 : HADDOCK 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 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. = 2.8 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 7 ILE A 85 -21.74 -157.99 REMARK 500 7 GLU A 95 22.76 -142.08 REMARK 500 7 GLU A 96 -47.43 -151.78 REMARK 500 7 PRO A 102 21.97 -77.59 REMARK 500 8 TYR A 27 -168.09 -128.01 REMARK 500 8 LYS A 31 -167.92 -108.28 REMARK 500 8 ASN A 34 -149.64 45.92 REMARK 500 8 LEU A 35 -66.58 -176.36 REMARK 500 8 ILE A 85 -21.81 -157.99 REMARK 500 8 GLU A 95 22.81 -142.04 REMARK 500 8 GLU A 96 -52.51 -151.86 REMARK 500 8 ASP A 97 144.31 177.14 REMARK 500 8 ARG A 106 -33.81 -159.23 REMARK 500 9 LYS A 31 -166.40 -107.53 REMARK 500 9 ASN A 34 75.45 35.84 REMARK 500 9 ILE A 85 -21.77 -157.95 REMARK 500 9 GLU A 95 22.80 -142.15 REMARK 500 9 GLU A 96 -46.66 -151.86 REMARK 500 9 ASP A 97 -104.21 -92.37 REMARK 500 9 LYS A 104 95.93 -166.30 REMARK 500 9 ARG A 106 -68.25 -139.58 REMARK 500 10 PRO A 26 -71.50 -61.47 REMARK 500 10 TYR A 27 -164.75 -120.53 REMARK 500 10 LYS A 31 -169.36 -117.05 REMARK 500 10 ASN A 34 76.08 32.39 REMARK 500 10 SER A 72 35.60 -170.36 REMARK 500 10 ALA A 73 -53.42 -128.37 REMARK 500 10 ILE A 85 -21.71 -158.05 REMARK 500 10 GLU A 95 22.79 -142.20 REMARK 500 10 GLU A 96 -50.74 -151.77 REMARK 500 10 LYS A 98 89.75 -151.10 REMARK 500 11 LYS A 31 -168.17 -119.08 REMARK 500 11 ASN A 34 75.26 31.62 REMARK 500 11 SER A 72 86.11 -153.44 REMARK 500 11 ILE A 85 -21.73 -158.01 REMARK 500 11 GLU A 95 22.77 -142.09 REMARK 500 11 GLU A 96 -47.34 -151.80 REMARK 500 12 LYS A 31 -166.79 -123.52 REMARK 500 12 ASN A 34 77.16 35.54 REMARK 500 12 ILE A 85 -21.81 -157.97 REMARK 500 12 GLU A 95 22.85 -142.15 REMARK 500 12 GLU A 96 -48.68 -151.80 REMARK 500 12 ARG A 106 -159.45 -120.40 REMARK 500 13 LYS A 31 -167.30 -125.75 REMARK 500 13 ASN A 34 89.11 36.32 REMARK 500 13 SER A 72 79.23 -153.84 REMARK 500 13 ILE A 85 -21.71 -157.98 REMARK 500 13 GLU A 95 22.93 -142.12 REMARK 500 13 GLU A 96 -48.52 -151.86 REMARK 500 13 ASP A 97 -167.47 -173.71 REMARK 500 13 LYS A 104 122.92 -170.96 REMARK 500 14 ASN A 34 80.29 33.47 REMARK 500 14 ALA A 73 -21.89 -163.28 REMARK 500 14 ILE A 85 -21.80 -157.96 REMARK 500 14 GLU A 95 22.87 -142.11 REMARK 500 14 GLU A 96 -48.09 -151.83 REMARK 500 15 LYS A 31 -164.85 -124.93 REMARK 500 15 GLN A 32 170.83 -59.75 REMARK 500 15 ASN A 34 80.46 36.50 REMARK 500 15 ILE A 85 -21.83 -157.95 REMARK 500 15 GLU A 95 22.84 -142.10 REMARK 500 15 GLU A 96 -48.06 -151.79 REMARK 500 16 TYR A 27 -165.67 -129.60 REMARK 500 16 ASN A 34 79.19 36.30 REMARK 500 16 SER A 72 15.17 -149.71 REMARK 500 16 ALA A 73 -63.93 -92.42 REMARK 500 16 ILE A 85 -21.71 -157.95 REMARK 500 16 GLU A 95 22.87 -142.10 REMARK 500 16 GLU A 96 -46.97 -151.79 REMARK 500 16 LYS A 98 127.18 -176.07 REMARK 500 17 ASN A 34 83.46 35.11 REMARK 500 17 SER A 72 11.49 176.08 REMARK 500 17 ILE A 85 -21.85 -157.93 REMARK 500 17 GLU A 95 22.86 -142.07 REMARK 500 17 GLU A 96 -48.21 -151.78 REMARK 500 17 ASP A 97 -121.62 -92.89 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, 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 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 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
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