PDB Short entry for 1QK9 HEADER METHYL-CPG-BINDING PROTEIN 12-JUL-99 1QK9 TITLE THE SOLUTION STRUCTURE OF THE DOMAIN FROM MECP2 THAT BINDS TO TITLE 2 METHYLATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-CPG-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MCPG BINDING DOMAIN OF MECP2; COMPND 5 SYNONYM: MBD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: INCLUSION BODIES; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET6HMBD KEYWDS METHYL-CPG-BINDING PROTEIN, SOLUTION STRUCTURE, METHYLATED DNA, KEYWDS 2 METHYL CYTOSINE, MBD EXPDTA SOLUTION NMR NUMMDL 28 AUTHOR R.I.D.WAKEFIELD,B.O.SMITH,X.NAN,A.FREE,A.SOTERIOU,D.UHRIN,A.P.BIRD, AUTHOR 2 P.N.BARLOW REVDAT 3 18-APR-18 1QK9 1 JRNL REVDAT 2 24-FEB-09 1QK9 1 VERSN REVDAT 1 08-OCT-99 1QK9 0 JRNL AUTH R.I.D.WAKEFIELD,B.O.SMITH,X.NAN,A.FREE,A.SOTERIOU,D.UHRIN, JRNL AUTH 2 A.P.BIRD,P.N.BARLOW JRNL TITL THE SOLUTION STRUCTURE OF THE DOMAIN FROM MECP2 THAT BINDS JRNL TITL 2 TO METHYLATED DNA JRNL REF J.MOL.BIOL. V. 291 1055 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10518942 JRNL DOI 10.1006/JMBI.1999.3023 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.HENDRICH,A.P.BIRD REMARK 1 TITL IDENTIFICATION AND CHARACTERISATION OF A FAMILY OF MAMMALIAN REMARK 1 TITL 2 METHYL-CPG BINDING PROTEINS REMARK 1 REF MOL.CELL.BIOL. V. 18 6538 1998 REMARK 1 REFN ISSN 0270-7306 REMARK 1 PMID 9774669 REMARK 1 REFERENCE 2 REMARK 1 AUTH X.S.NAN,H.-H.NG,C.A.JOHNSON,C.D.LAHERTY,B.M.TURNER, REMARK 1 AUTH 2 R.N.EISENMANN,A.BIRD REMARK 1 TITL TRANSCRIPTIONAL REPRESSION BY THE METHYL-CPG BINDING PROTEIN REMARK 1 TITL 2 MECP2 INVOLVES A HISTONE DEACETYLASE COMPLEX REMARK 1 REF NATURE V. 393 386 1998 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 9620804 REMARK 1 DOI 10.1038/30764 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.P.BIRD REMARK 1 TITL THE RELATIONSHIP OF DNA METHYLATION TO CANCER. REMARK 1 REF CANCER SURV. V. 28 87 1996 REMARK 1 REFN ISSN 0261-2429 REMARK 1 PMID 8977030 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.NILGES REMARK 1 TITL CALCULATION OF PROTEIN STRUCTURES WITH AMBIGUOUS DISTANCE REMARK 1 TITL 2 RESTRAINTS AUTOMATED ASSIGNMENT OF AMBIGUOUS NOE CROSSPEAKS REMARK 1 TITL 3 AND DISULFIDE CONNECTIVITIES REMARK 1 REF J.MOL.BIOL. V. 245 645 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7844833 REMARK 1 DOI 10.1006/JMBI.1994.0053 REMARK 1 REFERENCE 5 REMARK 1 AUTH J.BOYES,A.P.BIRD REMARK 1 TITL DNA METHYLATION INHIBITS TRANSCRIPTION INDIRECTLY VIA A REMARK 1 TITL 2 METHYL-CPG BINDING PROTEIN REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 64 1123 1991 REMARK 1 REFN ISSN 0092-8674 REMARK 1 PMID 2004419 REMARK 1 DOI 10.1016/0092-8674(91)90267-3 REMARK 1 REFERENCE 6 REMARK 1 AUTH A.P.BIRD REMARK 1 TITL CPG-RICH ISLANDS AND THE FUNCTION OF DNA METHYLATION REMARK 1 REF NATURE V. 321 209 1986 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 2423876 REMARK 1 DOI 10.1038/321209A0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AMBIGUOUS DISTANCE RESTRAINTS WERE USED REMARK 3 SEE M.NILGES CITATION REMARK 4 REMARK 4 1QK9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1290002784. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 291 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 90% H2O / 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; HNCA; REMARK 210 HNCOCA; CBCACONH; HNCACB; HCCH- REMARK 210 TOCSY; HCCONH-TOCSY; 15N-EDITTED REMARK 210 HSQC; 13C-EDITTED HSQC; HBHACONH; REMARK 210 15N-EDITTED HSQC-NOESY; 13C- REMARK 210 EDITTED HSQC-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, AZARA, ANSIG, XPLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 28 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 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 O TRP A 28 HH21 ARG A 30 1.53 REMARK 500 H ASN A 50 O LYS A 54 1.57 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 4 59.62 -159.65 REMARK 500 1 PRO A 5 -169.50 -58.86 REMARK 500 1 LYS A 6 89.32 43.09 REMARK 500 1 SER A 10 65.64 -164.62 REMARK 500 1 ILE A 12 40.06 -94.32 REMARK 500 1 ARG A 13 121.54 78.97 REMARK 500 1 ASP A 14 96.24 -45.54 REMARK 500 1 PRO A 17 -155.79 -79.62 REMARK 500 1 MET A 18 105.37 -171.71 REMARK 500 1 ASP A 20 73.19 -116.92 REMARK 500 1 THR A 23 50.06 -90.65 REMARK 500 1 PRO A 25 145.08 -22.79 REMARK 500 1 ARG A 39 -70.29 -107.60 REMARK 500 1 SER A 40 31.89 -98.72 REMARK 500 1 THR A 72 23.75 -149.86 REMARK 500 1 SER A 73 52.37 -152.88 REMARK 500 1 LEU A 74 -44.03 -154.53 REMARK 500 1 ASP A 75 100.81 63.66 REMARK 500 1 PHE A 81 77.93 -105.96 REMARK 500 1 THR A 84 46.14 -99.39 REMARK 500 1 ARG A 86 -156.00 -145.74 REMARK 500 2 SER A 2 88.60 58.56 REMARK 500 2 SER A 4 71.78 -157.07 REMARK 500 2 LYS A 6 79.14 -110.69 REMARK 500 2 ILE A 12 52.60 -93.43 REMARK 500 2 ARG A 13 82.08 54.81 REMARK 500 2 ASP A 14 50.05 -115.16 REMARK 500 2 TYR A 19 -70.13 -67.18 REMARK 500 2 ASP A 20 79.61 -64.08 REMARK 500 2 THR A 23 49.60 -87.97 REMARK 500 2 PRO A 25 169.24 -45.43 REMARK 500 2 LYS A 36 -71.49 -105.02 REMARK 500 2 SER A 37 -81.97 64.29 REMARK 500 2 ALA A 41 179.32 -52.53 REMARK 500 2 THR A 72 22.87 -145.95 REMARK 500 2 LEU A 74 -43.48 -144.39 REMARK 500 2 ASP A 75 107.90 62.80 REMARK 500 2 ARG A 86 -154.11 -136.23 REMARK 500 2 SER A 88 20.39 -147.17 REMARK 500 2 SER A 90 119.33 62.36 REMARK 500 3 SER A 4 -64.44 -163.55 REMARK 500 3 LYS A 6 -158.99 -108.44 REMARK 500 3 GLN A 7 87.11 63.09 REMARK 500 3 SER A 10 80.67 -160.70 REMARK 500 3 ARG A 13 175.63 63.87 REMARK 500 3 PRO A 17 -164.77 -77.18 REMARK 500 3 MET A 18 -40.58 -157.92 REMARK 500 3 TYR A 19 -65.89 75.14 REMARK 500 3 ASP A 20 89.30 -65.57 REMARK 500 3 PRO A 25 166.64 -40.79 REMARK 500 REMARK 500 THIS ENTRY HAS 504 RAMACHANDRAN OUTLIERS. 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 11 ASN A 50 -12.99 REMARK 500 15 ASN A 50 -12.96 REMARK 500 18 ASN A 50 -12.37 REMARK 500 19 ASN A 50 -12.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. DBREF 1QK9 A 1 92 UNP P51608 MEC2_HUMAN 77 168 SEQADV 1QK9 GLY A 89 UNP P51608 PRO 165 CONFLICT SEQADV 1QK9 GLY A 91 UNP P51608 ARG 167 CONFLICT SEQADV 1QK9 CYS A 92 UNP P51608 ARG 168 CONFLICT SEQRES 1 A 92 ALA SER ALA SER PRO LYS GLN ARG ARG SER ILE ILE ARG SEQRES 2 A 92 ASP ARG GLY PRO MET TYR ASP ASP PRO THR LEU PRO GLU SEQRES 3 A 92 GLY TRP THR ARG LYS LEU LYS GLN ARG LYS SER GLY ARG SEQRES 4 A 92 SER ALA GLY LYS TYR ASP VAL TYR LEU ILE ASN PRO GLN SEQRES 5 A 92 GLY LYS ALA PHE ARG SER LYS VAL GLU LEU ILE ALA TYR SEQRES 6 A 92 PHE GLU LYS VAL GLY ASP THR SER LEU ASP PRO ASN ASP SEQRES 7 A 92 PHE ASP PHE THR VAL THR GLY ARG GLY SER GLY SER GLY SEQRES 8 A 92 CYS HELIX 1 HEL VAL A 60 GLY A 70 1 11 HELIX 2 HEL ASP A 75 ASP A 78 5 4 SHEET 1 A 3 THR A 29 LEU A 32 0 SHEET 2 A 3 VAL A 46 ASN A 50 -1 N THR A 29 O ILE A 49 SHEET 3 A 3 LYS A 54 ARG A 57 -1 N ILE A 49 O PHE A 56 CISPEP 1 GLY A 16 PRO A 17 2 1.16 CISPEP 2 SER A 4 PRO A 5 3 -1.71 CISPEP 3 GLY A 16 PRO A 17 3 2.33 CISPEP 4 GLY A 16 PRO A 17 4 3.78 CISPEP 5 GLY A 16 PRO A 17 5 -3.22 CISPEP 6 ASP A 21 PRO A 22 6 -8.24 CISPEP 7 SER A 4 PRO A 5 7 -1.03 CISPEP 8 GLY A 16 PRO A 17 7 3.30 CISPEP 9 ASP A 21 PRO A 22 7 -10.60 CISPEP 10 ASP A 21 PRO A 22 8 -5.42 CISPEP 11 ASP A 75 PRO A 76 9 17.86 CISPEP 12 ASP A 21 PRO A 22 10 -6.48 CISPEP 13 ASN A 50 PRO A 51 11 -26.70 CISPEP 14 ASP A 21 PRO A 22 13 -13.97 CISPEP 15 ASP A 21 PRO A 22 14 -7.00 CISPEP 16 GLY A 16 PRO A 17 15 -1.88 CISPEP 17 ASN A 50 PRO A 51 15 -25.42 CISPEP 18 GLY A 16 PRO A 17 16 2.54 CISPEP 19 ASP A 21 PRO A 22 16 -2.97 CISPEP 20 GLY A 16 PRO A 17 17 -3.18 CISPEP 21 ASP A 75 PRO A 76 17 17.71 CISPEP 22 SER A 4 PRO A 5 18 2.08 CISPEP 23 ASN A 50 PRO A 51 18 -24.95 CISPEP 24 GLY A 16 PRO A 17 19 -2.28 CISPEP 25 ASN A 50 PRO A 51 19 -23.71 CISPEP 26 GLY A 16 PRO A 17 20 2.74 CISPEP 27 ASP A 75 PRO A 76 20 4.13 CISPEP 28 GLY A 16 PRO A 17 21 -4.14 CISPEP 29 ASP A 21 PRO A 22 21 -2.81 CISPEP 30 SER A 4 PRO A 5 22 -1.51 CISPEP 31 GLY A 16 PRO A 17 24 -2.29 CISPEP 32 GLY A 16 PRO A 17 25 2.78 CISPEP 33 SER A 4 PRO A 5 26 2.41 CISPEP 34 GLY A 16 PRO A 17 27 4.53 CISPEP 35 SER A 4 PRO A 5 28 -2.23 CISPEP 36 GLY A 16 PRO A 17 28 3.26 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