HEADER DNA BINDING PROTEIN 08-OCT-20 7D8K TITLE SOLUTION STRUCTURE OF THE METHYL-CPG BINDING DOMAIN OF MBD6 FROM TITLE 2 ARABIDOPSIS THALIANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN-CONTAINING PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MBD06,METHYL-CPG-BINDING PROTEIN MBD6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: MBD6, AT5G59380, F2O15.4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYL-CPG BINDING, GENE REPRESSOR, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.MAHANA,I.OHKI,E.WALINDA,D.MORIMOTO,K.SUGASE,M.SHIRAKAWA REVDAT 4 15-MAY-24 7D8K 1 REMARK REVDAT 3 14-JUN-23 7D8K 1 REMARK REVDAT 2 23-FEB-22 7D8K 1 JRNL REVDAT 1 20-OCT-21 7D8K 0 JRNL AUTH Y.MAHANA,I.OHKI,E.WALINDA,D.MORIMOTO,K.SUGASE,M.SHIRAKAWA JRNL TITL STRUCTURAL INSIGHTS INTO METHYLATED DNA RECOGNITION BY THE JRNL TITL 2 METHYL-CPG BINDING DOMAIN OF MBD6 FROM ARABIDOPSIS THALIANA JRNL TITL 3 . JRNL REF ACS OMEGA V. 7 3212 2022 JRNL REFN ESSN 2470-1343 JRNL PMID 35128234 JRNL DOI 10.1021/ACSOMEGA.1C04917 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7D8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1300018232. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-13C; U-15N] ATMBD6 MBD REMARK 210 DOMAIN, 20 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 0.5 MM [U-13C; U-15N] REMARK 210 ATMBD6 MBD DOMAIN, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 95% H2O/5% D2O; 0.5 MM [U-13C; REMARK 210 U-15N] ATMBD6 MBD DOMAIN, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 4 % C12E5, 1.2 % 1- REMARK 210 HEXANOL, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 2D 1H-13C HSQC ALIPHATIC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D REMARK 210 CC(CO)NH; 3D H(CC)(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HBHANH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 2D (HB) REMARK 210 CB(CGCD)HD; 2D (HB)CB(CGCDCE)HE; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D IPAP 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, TALOS+, MAGRO-NMRVIEW, REMARK 210 CCPNMR ANALYSIS, TOPSPIN, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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: 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: 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 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 H GLU A 107 O ARG A 112 1.60 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 SER A 100 -159.45 -91.32 REMARK 500 1 THR A 128 161.45 171.55 REMARK 500 2 ASN A 79 28.16 37.22 REMARK 500 2 TRP A 80 -3.63 -141.84 REMARK 500 2 SER A 129 63.95 -160.27 REMARK 500 2 ARG A 131 -79.36 157.08 REMARK 500 2 ASN A 138 49.34 -84.74 REMARK 500 3 ASN A 79 22.91 37.36 REMARK 500 3 ALA A 98 -135.10 -125.75 REMARK 500 3 THR A 128 83.70 -55.47 REMARK 500 4 ASN A 79 41.69 -89.22 REMARK 500 4 PRO A 83 85.18 -67.11 REMARK 500 4 LYS A 135 141.79 174.73 REMARK 500 4 ALA A 136 48.44 29.24 REMARK 500 5 SER A 77 -8.63 77.58 REMARK 500 5 ASN A 79 38.92 -83.35 REMARK 500 5 PRO A 83 84.93 -69.60 REMARK 500 5 ALA A 98 131.34 -20.85 REMARK 500 5 LYS A 130 -54.38 -124.55 REMARK 500 5 LYS A 134 108.31 -31.96 REMARK 500 6 ASN A 79 23.22 35.28 REMARK 500 6 PRO A 83 82.84 -57.92 REMARK 500 6 SER A 100 -166.87 -52.89 REMARK 500 6 ARG A 131 27.21 39.49 REMARK 500 7 ALA A 98 106.79 -17.16 REMARK 500 7 SER A 100 -148.62 -76.55 REMARK 500 7 THR A 128 170.36 82.12 REMARK 500 7 ARG A 131 -101.28 -142.47 REMARK 500 7 GLU A 137 12.69 80.99 REMARK 500 8 ASN A 79 -19.46 72.19 REMARK 500 8 ALA A 98 135.51 -29.49 REMARK 500 8 THR A 128 26.38 84.20 REMARK 500 8 SER A 129 24.51 86.83 REMARK 500 8 ARG A 131 85.16 -54.68 REMARK 500 9 ASP A 78 -61.55 -94.48 REMARK 500 9 ASN A 79 27.51 36.24 REMARK 500 9 ALA A 98 -166.08 -179.68 REMARK 500 9 SER A 100 -162.68 -60.49 REMARK 500 10 SER A 77 29.12 40.40 REMARK 500 10 THR A 128 55.25 77.12 REMARK 500 10 SER A 129 82.51 58.48 REMARK 500 10 LYS A 134 135.82 -173.90 REMARK 500 10 ASN A 138 -42.09 75.71 REMARK 500 11 ASN A 79 38.84 -71.13 REMARK 500 11 PRO A 83 86.74 -69.21 REMARK 500 11 ALA A 98 146.90 -37.44 REMARK 500 11 SER A 129 -97.44 -36.65 REMARK 500 11 ARG A 131 170.97 174.00 REMARK 500 12 LEU A 75 -140.10 37.31 REMARK 500 12 ASN A 79 44.78 -87.71 REMARK 500 REMARK 500 THIS ENTRY HAS 105 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27436 RELATED DB: BMRB DBREF 7D8K A 78 140 UNP Q9LTJ1 MBD6_ARATH 78 140 SEQADV 7D8K GLY A 73 UNP Q9LTJ1 EXPRESSION TAG SEQADV 7D8K PRO A 74 UNP Q9LTJ1 EXPRESSION TAG SEQADV 7D8K LEU A 75 UNP Q9LTJ1 EXPRESSION TAG SEQADV 7D8K GLY A 76 UNP Q9LTJ1 EXPRESSION TAG SEQADV 7D8K SER A 77 UNP Q9LTJ1 EXPRESSION TAG SEQRES 1 A 68 GLY PRO LEU GLY SER ASP ASN TRP LEU PRO PRO GLY TRP SEQRES 2 A 68 ARG VAL GLU ASP LYS ILE ARG THR SER GLY ALA THR ALA SEQRES 3 A 68 GLY SER VAL ASP LYS TYR TYR TYR GLU PRO ASN THR GLY SEQRES 4 A 68 ARG LYS PHE ARG SER ARG THR GLU VAL LEU TYR TYR LEU SEQRES 5 A 68 GLU HIS GLY THR SER LYS ARG GLY THR LYS LYS ALA GLU SEQRES 6 A 68 ASN THR TYR HELIX 1 AA1 SER A 116 GLY A 127 1 12 SHEET 1 AA1 3 ARG A 86 ILE A 91 0 SHEET 2 AA1 3 VAL A 101 GLU A 107 -1 O TYR A 106 N ARG A 86 SHEET 3 AA1 3 ARG A 112 PHE A 114 -1 O ARG A 112 N GLU A 107 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