HEADER TRANSCRIPTION 01-OCT-12 4HCZ TITLE PHF1 TUDOR IN COMPLEX WITH H3K36ME3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: TUDOR DOMAIN; COMPND 5 SYNONYM: PROTEIN PHF1, POLYCOMB-LIKE PROTEIN 1, HPCL1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: H3L-LIKE HISTONE; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: H3K36ME3; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PHF1, PCL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 OTHER_DETAILS: SYNTHETIC HUMAN H3K36ME3 PEPTIDE KEYWDS PROTEIN-PEPTIDE COMPLEX, TUDOR, HISTONE BINDING, H3K36ME3, NA, KEYWDS 2 NUCLEUS, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.A.MUSSELMAN,S.ROY,J.NUNEZ,T.G.KUTATELADZE REVDAT 3 20-SEP-23 4HCZ 1 LINK REVDAT 2 19-DEC-12 4HCZ 1 JRNL REVDAT 1 14-NOV-12 4HCZ 0 JRNL AUTH C.A.MUSSELMAN,N.AVVAKUMOV,R.WATANABE,C.G.ABRAHAM, JRNL AUTH 2 M.E.LALONDE,Z.HONG,C.ALLEN,S.ROY,J.K.NUNEZ,J.NICKOLOFF, JRNL AUTH 3 C.A.KULESZA,A.YASUI,J.COTE,T.G.KUTATELADZE JRNL TITL MOLECULAR BASIS FOR H3K36ME3 RECOGNITION BY THE TUDOR DOMAIN JRNL TITL 2 OF PHF1. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1266 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23142980 JRNL DOI 10.1038/NSMB.2435 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 12073 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.4144 - 2.9353 0.95 2917 151 0.1886 0.2066 REMARK 3 2 2.9353 - 2.3305 0.99 2977 129 0.2031 0.2705 REMARK 3 3 2.3305 - 2.0361 0.99 2932 156 0.2061 0.2511 REMARK 3 4 2.0361 - 1.8500 0.91 2667 144 0.2898 0.3932 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 60.87 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.33040 REMARK 3 B22 (A**2) : -5.08270 REMARK 3 B33 (A**2) : 8.41300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.23100 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1085 REMARK 3 ANGLE : 1.060 1473 REMARK 3 CHIRALITY : 0.071 161 REMARK 3 PLANARITY : 0.004 183 REMARK 3 DIHEDRAL : 14.919 409 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -0.3947 -1.4904 24.6741 REMARK 3 T TENSOR REMARK 3 T11: 0.1690 T22: 0.1649 REMARK 3 T33: 0.1609 T12: 0.0084 REMARK 3 T13: 0.0061 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 1.2675 L22: 1.3977 REMARK 3 L33: 0.6479 L12: 0.2667 REMARK 3 L13: 0.6046 L23: 0.8212 REMARK 3 S TENSOR REMARK 3 S11: -0.0042 S12: 0.0173 S13: 0.1757 REMARK 3 S21: -0.0297 S22: 0.0397 S23: 0.1476 REMARK 3 S31: -0.0169 S32: -0.0492 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12091 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 23.413 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2E5P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 20% PEG 10000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.01500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.83500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.01500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.83500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY B 85 REMARK 465 SER D 31 REMARK 465 THR D 32 REMARK 465 GLY D 33 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG D 40 CG CD NE CZ NH1 NH2 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 ASP A 68 -2.30 77.54 REMARK 500 ASP B 68 -0.60 74.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 4HCZ A 28 85 UNP O43189 PHF1_HUMAN 28 85 DBREF 4HCZ B 28 85 UNP O43189 PHF1_HUMAN 28 85 DBREF 4HCZ C 31 40 UNP Q6TXQ4 Q6TXQ4_HUMAN 17 26 DBREF 4HCZ D 31 40 UNP Q6TXQ4 Q6TXQ4_HUMAN 17 26 SEQRES 1 A 58 ARG PRO ARG LEU TRP GLU GLY GLN ASP VAL LEU ALA ARG SEQRES 2 A 58 TRP THR ASP GLY LEU LEU TYR LEU GLY THR ILE LYS LYS SEQRES 3 A 58 VAL ASP SER ALA ARG GLU VAL CYS LEU VAL GLN PHE GLU SEQRES 4 A 58 ASP ASP SER GLN PHE LEU VAL LEU TRP LYS ASP ILE SER SEQRES 5 A 58 PRO ALA ALA LEU PRO GLY SEQRES 1 B 58 ARG PRO ARG LEU TRP GLU GLY GLN ASP VAL LEU ALA ARG SEQRES 2 B 58 TRP THR ASP GLY LEU LEU TYR LEU GLY THR ILE LYS LYS SEQRES 3 B 58 VAL ASP SER ALA ARG GLU VAL CYS LEU VAL GLN PHE GLU SEQRES 4 B 58 ASP ASP SER GLN PHE LEU VAL LEU TRP LYS ASP ILE SER SEQRES 5 B 58 PRO ALA ALA LEU PRO GLY SEQRES 1 C 10 SER THR GLY GLY VAL M3L LYS PRO HIS ARG SEQRES 1 D 10 SER THR GLY GLY VAL M3L LYS PRO HIS ARG MODRES 4HCZ M3L C 36 LYS N-TRIMETHYLLYSINE MODRES 4HCZ M3L D 36 LYS N-TRIMETHYLLYSINE HET M3L C 36 12 HET M3L D 36 12 HETNAM M3L N-TRIMETHYLLYSINE FORMUL 3 M3L 2(C9 H21 N2 O2 1+) FORMUL 5 HOH *161(H2 O) SHEET 1 A 5 GLN A 70 LEU A 74 0 SHEET 2 A 5 VAL A 60 PHE A 65 -1 N VAL A 63 O PHE A 71 SHEET 3 A 5 LEU A 46 ASP A 55 -1 N LYS A 52 O LEU A 62 SHEET 4 A 5 ASP A 36 ARG A 40 -1 N VAL A 37 O GLY A 49 SHEET 5 A 5 ILE A 78 PRO A 80 -1 O SER A 79 N LEU A 38 SHEET 1 B 5 GLN B 70 LEU B 74 0 SHEET 2 B 5 VAL B 60 PHE B 65 -1 N VAL B 63 O PHE B 71 SHEET 3 B 5 LEU B 46 ASP B 55 -1 N LYS B 52 O LEU B 62 SHEET 4 B 5 ASP B 36 ARG B 40 -1 N VAL B 37 O GLY B 49 SHEET 5 B 5 ILE B 78 PRO B 80 -1 O SER B 79 N LEU B 38 LINK C VAL C 35 N M3L C 36 1555 1555 1.33 LINK C M3L C 36 N LYS C 37 1555 1555 1.33 LINK C VAL D 35 N M3L D 36 1555 1555 1.32 LINK C M3L D 36 N LYS D 37 1555 1555 1.32 CISPEP 1 LEU B 83 PRO B 84 0 3.84 CRYST1 88.030 29.670 62.000 90.00 116.41 90.00 C 1 2 1 8 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 0.011360 0.000000 0.005642 0.00000 SCALE2 0.000000 0.033704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018009 0.00000