HEADER DNA BINDING PROTEIN 27-JUL-18 6ACV TITLE THE SOLUTION NMR STRUCTURE OF MBD DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING DOMAIN-CONTAINING PROTEIN 11; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MBD DOMAIN; COMPND 5 SYNONYM: MBD11,METHYL-CPG-BINDING PROTEIN MBD11; COMPND 6 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: MBD11, AT3G15790, MSJ11.19; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BIND METHYL-CG AND TG SITES IN DNA, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.L.LI,Y.Y.FENG,Y.ZHOU,Y.M.DING,K.LIU,Y.NIE,F.LI,Y.Y.YANG REVDAT 2 14-JUN-23 6ACV 1 REMARK REVDAT 1 31-JUL-19 6ACV 0 JRNL AUTH S.L.LI,Y.Y.FENG,Y.ZHOU,Y.M.DING,K.LIU,Y.NIE,F.LI,Y.Y.YANG JRNL TITL THE SOLUTION NMR STRUCTURE OF MBD DOMAINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ACV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008504. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 8.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 150 MM SODIUM CHLORIDE, 20 MM REMARK 210 TRIS, 1 MM DTT, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HBHA(CO)NH; 3D C(CO)NH; REMARK 210 3D H(CCO)NH; 3D 15N_NOESY; 3D REMARK 210 13C_NOESY_ALI; 3D 13C_NOESY_ARO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0, SPARKY, TOPSPIN 3.5, REMARK 210 NMRPIPE 2008 REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 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 HIS A 2 -55.91 -129.60 REMARK 500 1 HIS A 3 84.44 61.31 REMARK 500 1 PHE A 16 38.05 -96.85 REMARK 500 1 ALA A 21 179.59 65.81 REMARK 500 1 SER A 22 -152.30 61.01 REMARK 500 1 TRP A 39 -168.38 -105.03 REMARK 500 1 ASN A 46 -84.39 -153.35 REMARK 500 1 LYS A 47 -79.08 -135.65 REMARK 500 1 VAL A 48 -72.34 -128.38 REMARK 500 1 LYS A 53 151.00 64.04 REMARK 500 2 HIS A 3 -50.44 -153.90 REMARK 500 2 HIS A 4 153.68 69.73 REMARK 500 2 GLU A 26 -87.49 59.58 REMARK 500 2 GLU A 55 -172.97 -69.07 REMARK 500 2 GLU A 64 71.31 -112.96 REMARK 500 3 HIS A 3 -66.73 -136.06 REMARK 500 3 LEU A 14 -47.89 -162.78 REMARK 500 3 TYR A 15 -71.27 -143.92 REMARK 500 3 MET A 20 95.26 62.85 REMARK 500 3 SER A 24 107.75 68.70 REMARK 500 3 GLU A 27 99.81 -66.92 REMARK 500 3 VAL A 48 -63.68 -131.13 REMARK 500 3 GLU A 55 -169.52 -75.60 REMARK 500 4 SER A 9 -45.23 -160.41 REMARK 500 4 PHE A 16 -1.88 66.62 REMARK 500 4 GLU A 26 114.81 -167.69 REMARK 500 4 LYS A 52 88.65 -66.93 REMARK 500 4 SER A 93 105.55 -58.59 REMARK 500 5 HIS A 3 -175.62 64.03 REMARK 500 5 HIS A 6 31.49 -142.49 REMARK 500 5 SER A 8 97.93 -63.92 REMARK 500 5 TYR A 15 -84.73 -141.95 REMARK 500 5 ALA A 21 -77.18 -79.88 REMARK 500 5 SER A 22 164.32 179.95 REMARK 500 5 SER A 50 -66.22 71.74 REMARK 500 6 HIS A 3 -39.82 -155.52 REMARK 500 6 HIS A 6 112.76 -164.38 REMARK 500 6 GLN A 17 80.86 56.42 REMARK 500 6 MET A 20 -67.42 69.17 REMARK 500 6 GLU A 26 -171.27 58.31 REMARK 500 6 SER A 30 113.48 -161.99 REMARK 500 6 LYS A 52 77.33 -65.41 REMARK 500 6 GLU A 55 -165.92 -73.37 REMARK 500 6 GLU A 64 75.74 -69.63 REMARK 500 6 THR A 92 31.72 -77.88 REMARK 500 7 HIS A 7 81.50 -155.11 REMARK 500 7 ARG A 11 -57.72 -130.79 REMARK 500 7 GLU A 12 160.68 69.08 REMARK 500 7 ASN A 13 96.84 72.05 REMARK 500 7 PHE A 16 87.70 49.70 REMARK 500 REMARK 500 THIS ENTRY HAS 163 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36204 RELATED DB: BMRB REMARK 900 THE SOLUTION NMR STRUCTURE OF MBD DOMAIN DBREF 6ACV A 25 95 UNP Q9LW00 MBD11_ARATH 4 74 SEQADV 6ACV MET A 1 UNP Q9LW00 INITIATING METHIONINE SEQADV 6ACV HIS A 2 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV HIS A 3 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV HIS A 4 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV HIS A 5 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV HIS A 6 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV HIS A 7 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV SER A 8 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV SER A 9 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV GLY A 10 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV ARG A 11 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV GLU A 12 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV ASN A 13 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV LEU A 14 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV TYR A 15 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV PHE A 16 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV GLN A 17 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV GLY A 18 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV HIS A 19 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV MET A 20 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV ALA A 21 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV SER A 22 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV GLY A 23 UNP Q9LW00 EXPRESSION TAG SEQADV 6ACV SER A 24 UNP Q9LW00 EXPRESSION TAG SEQRES 1 A 95 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 95 LEU TYR PHE GLN GLY HIS MET ALA SER GLY SER GLU GLU SEQRES 3 A 95 GLU VAL VAL SER VAL GLU LEU PRO ALA PRO SER SER TRP SEQRES 4 A 95 LYS LYS LEU PHE TYR PRO ASN LYS VAL GLY SER VAL LYS SEQRES 5 A 95 LYS THR GLU VAL VAL PHE VAL ALA PRO THR GLY GLU GLU SEQRES 6 A 95 ILE SER ASN ARG LYS GLN LEU GLU GLN TYR LEU LYS SER SEQRES 7 A 95 HIS PRO GLY ASN PRO ALA ILE ALA GLU PHE ASP TRP THR SEQRES 8 A 95 THR SER GLY THR HELIX 1 AA1 ASN A 68 HIS A 79 1 12 HELIX 2 AA2 ALA A 84 PHE A 88 5 5 SHEET 1 AA1 2 LYS A 40 LEU A 42 0 SHEET 2 AA1 2 VAL A 57 VAL A 59 -1 O VAL A 59 N LYS A 40 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