HEADER PROTEIN BINDING 07-JAN-11 2L89 TITLE SOLUTION STRUCTURE OF PDP1 PWWP DOMAIN REVEALS ITS UNIQUE BINDING TITLE 2 SITES FOR METHYLATED H4K20 AND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PWWP DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PWWP DOMAIN, RESIDUES 45-152; COMPND 5 SYNONYM: SET9-ASSOCIATED FACTOR PDP1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET22B KEYWDS HISTONE BINDING, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.QIU,J.ZHANG,W.ZHANG REVDAT 3 15-MAY-24 2L89 1 REMARK REVDAT 2 14-JUN-23 2L89 1 SEQADV REVDAT 1 21-DEC-11 2L89 0 JRNL AUTH Y.QIU,W.ZHANG,C.ZHAO,Y.WANG,W.WANG,J.ZHANG,Z.ZHANG,G.LI, JRNL AUTH 2 Y.SHI,X.TU,J.WU JRNL TITL SOLUTION STRUCTURE OF PDP1 PWWP DOMAIN REVEALS ITS UNIQUE JRNL TITL 2 BINDING SITES FOR METHYLATED H4K20 AND DNA JRNL REF BIOCHEM.J. 2011 JRNL REFN ESSN 1470-8728 JRNL PMID 22150589 JRNL DOI 10.1042/BJ20111885 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 2L89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000102080. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.8 REMARK 210 IONIC STRENGTH : 0.140 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20MM SODIUM PHOSPHATE-1; 100MM REMARK 210 SODIUM CHLORIDE-2; 2MM EDTA-3; REMARK 210 90% H2O/10% D2O; 20MM SODIUM REMARK 210 PHOSPHATE-4; 100MM SODIUM REMARK 210 CHLORIDE-5; 2MM EDTA-6; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D C(CO)NH; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HN(CO) REMARK 210 CA; 3D H(CCO)NH; 3D 1H-15N NOESY; REMARK 210 3D HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 1H-13C NOESY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 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 PRO A 61 103.84 -58.21 REMARK 500 1 PRO A 64 -168.75 -65.14 REMARK 500 1 SER A 79 -79.34 -165.73 REMARK 500 1 LEU A 80 27.77 -153.57 REMARK 500 1 ASN A 83 27.41 -145.55 REMARK 500 1 SER A 84 -73.37 -123.72 REMARK 500 1 PHE A 98 82.06 -57.88 REMARK 500 1 ASN A 99 -169.46 -129.80 REMARK 500 1 SER A 123 38.95 -93.27 REMARK 500 1 LYS A 124 -53.21 -130.11 REMARK 500 1 SER A 148 -75.35 -156.86 REMARK 500 1 THR A 149 96.59 57.37 REMARK 500 1 ASP A 150 171.17 69.17 REMARK 500 2 ALA A 46 153.62 68.94 REMARK 500 2 ARG A 49 -176.17 -173.75 REMARK 500 2 LEU A 50 75.27 60.81 REMARK 500 2 PRO A 61 98.12 -63.45 REMARK 500 2 ASP A 78 -76.13 -95.09 REMARK 500 2 SER A 79 -74.64 -142.52 REMARK 500 2 LEU A 80 -74.78 -152.04 REMARK 500 2 ASN A 81 39.14 -157.42 REMARK 500 2 THR A 82 40.54 -145.21 REMARK 500 2 ASN A 83 -51.01 -165.66 REMARK 500 2 SER A 84 -47.12 -169.25 REMARK 500 2 SER A 85 108.65 66.84 REMARK 500 2 PHE A 86 104.59 66.57 REMARK 500 2 PHE A 98 28.14 80.66 REMARK 500 2 ASN A 99 -161.98 -78.78 REMARK 500 2 ALA A 101 125.73 -172.91 REMARK 500 2 SER A 122 68.14 -116.11 REMARK 500 2 SER A 123 43.41 -92.27 REMARK 500 2 THR A 139 106.54 -51.67 REMARK 500 2 LEU A 143 -88.88 65.81 REMARK 500 2 LYS A 144 -75.76 58.14 REMARK 500 2 LEU A 151 -65.65 -143.38 REMARK 500 3 ASP A 47 31.38 -151.10 REMARK 500 3 ASP A 48 66.91 -102.35 REMARK 500 3 LEU A 50 94.25 67.56 REMARK 500 3 PRO A 64 -179.86 -67.82 REMARK 500 3 ASP A 78 68.74 61.95 REMARK 500 3 LEU A 80 -86.48 -106.49 REMARK 500 3 ASN A 81 37.06 -166.17 REMARK 500 3 SER A 85 131.35 -171.67 REMARK 500 3 LYS A 91 98.86 -68.11 REMARK 500 3 PHE A 98 76.51 75.89 REMARK 500 3 ASN A 99 -157.88 -135.02 REMARK 500 3 SER A 123 -33.86 80.91 REMARK 500 3 THR A 139 106.76 -42.76 REMARK 500 3 ASP A 142 -75.92 -64.94 REMARK 500 3 GLU A 146 -69.58 -157.58 REMARK 500 REMARK 500 THIS ENTRY HAS 310 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17398 RELATED DB: BMRB DBREF 2L89 A 45 152 UNP O59676 PDP1_SCHPO 45 152 SEQADV 2L89 LEU A 151 UNP O59676 GLU 151 CLONING ARTIFACT SEQRES 1 A 108 SER ALA ASP ASP ARG LEU ASN PHE GLY ASP ARG ILE LEU SEQRES 2 A 108 VAL LYS ALA PRO GLY TYR PRO TRP TRP PRO ALA LEU LEU SEQRES 3 A 108 LEU ARG ARG LYS GLU THR LYS ASP SER LEU ASN THR ASN SEQRES 4 A 108 SER SER PHE ASN VAL LEU TYR LYS VAL LEU PHE PHE PRO SEQRES 5 A 108 ASP PHE ASN PHE ALA TRP VAL LYS ARG ASN SER VAL LYS SEQRES 6 A 108 PRO LEU LEU ASP SER GLU ILE ALA LYS PHE LEU GLY SER SEQRES 7 A 108 SER LYS ARG LYS SER LYS GLU LEU ILE GLU ALA TYR GLU SEQRES 8 A 108 ALA SER LYS THR PRO PRO ASP LEU LYS GLU GLU SER SER SEQRES 9 A 108 THR ASP LEU GLU HELIX 1 1 LYS A 104 ASN A 106 5 3 HELIX 2 2 LEU A 112 SER A 122 1 11 HELIX 3 3 SER A 127 LYS A 138 1 12 HELIX 4 4 THR A 139 LEU A 143 5 5 SHEET 1 A 5 ASN A 99 VAL A 103 0 SHEET 2 A 5 PHE A 86 PHE A 94 -1 N TYR A 90 O VAL A 103 SHEET 3 A 5 TRP A 65 LYS A 77 -1 N LEU A 71 O LYS A 91 SHEET 4 A 5 ASP A 54 LYS A 59 -1 N VAL A 58 O TRP A 66 SHEET 5 A 5 VAL A 108 PRO A 110 -1 O LYS A 109 N LEU A 57 CISPEP 1 PHE A 95 PRO A 96 1 -0.23 CISPEP 2 PHE A 95 PRO A 96 2 0.28 CISPEP 3 PHE A 95 PRO A 96 3 0.10 CISPEP 4 PHE A 95 PRO A 96 4 -0.01 CISPEP 5 PHE A 95 PRO A 96 5 0.15 CISPEP 6 PHE A 95 PRO A 96 6 0.19 CISPEP 7 PHE A 95 PRO A 96 7 -0.28 CISPEP 8 PHE A 95 PRO A 96 8 0.05 CISPEP 9 PHE A 95 PRO A 96 9 -0.15 CISPEP 10 PHE A 95 PRO A 96 10 0.01 CISPEP 11 PHE A 95 PRO A 96 11 -0.27 CISPEP 12 PHE A 95 PRO A 96 12 -0.04 CISPEP 13 PHE A 95 PRO A 96 13 -0.03 CISPEP 14 PHE A 95 PRO A 96 14 0.22 CISPEP 15 PHE A 95 PRO A 96 15 -0.16 CISPEP 16 PHE A 95 PRO A 96 16 -0.12 CISPEP 17 PHE A 95 PRO A 96 17 0.03 CISPEP 18 PHE A 95 PRO A 96 18 0.06 CISPEP 19 PHE A 95 PRO A 96 19 -0.18 CISPEP 20 PHE A 95 PRO A 96 20 -0.30 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