Header list of 1qk9.pdb file
Complete list - r 18 2 Bytes
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
MODEL 1
Complete list - r 18 2 Bytes