HEADER TRANSCRIPTION 27-AUG-17 6AT0 TITLE CHROMODOMAIN HP1 WITH A P-NITRO-L-PHENYLALANINE MUTATION AT POSITION TITLE 2 24 BOUND TO HISTONE H3 PEPTIDE CONTAINING TRIMETHYL LYSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROCHROMATIN PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CHROMO 1 DOMAIN, RESIDUES 17-76; COMPND 5 SYNONYM: HP1,NON-HISTONE CHROMOSOMAL PROTEIN C1A9 ANTIGEN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRIMETHYL LYSINE HISTONE H3 TAIL PEPTIDE; COMPND 10 CHAIN: P; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: SU(VAR)205, HP1, CG8409; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 12 ORGANISM_TAXID: 7227 KEYWDS HISTONE READER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.M.BRUSTAD,S.A.BARIL,M.L.WATERS REVDAT 3 04-OCT-23 6AT0 1 REMARK REVDAT 2 13-DEC-17 6AT0 1 JRNL REVDAT 1 06-DEC-17 6AT0 0 JRNL AUTH S.A.BARIL,A.L.KOENIG,M.W.KRONE,K.I.ALBANESE,C.Q.HE,G.Y.LEE, JRNL AUTH 2 K.N.HOUK,M.L.WATERS,E.M.BRUSTAD JRNL TITL INVESTIGATION OF TRIMETHYLLYSINE BINDING BY THE HP1 JRNL TITL 2 CHROMODOMAIN VIA UNNATURAL AMINO ACID MUTAGENESIS. JRNL REF J. AM. CHEM. SOC. V. 139 17253 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 29111699 JRNL DOI 10.1021/JACS.7B09223 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 25429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1291 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 11.2242 - 2.6613 0.96 2818 129 0.2045 0.2403 REMARK 3 2 2.6613 - 2.1170 0.98 2752 149 0.2180 0.2363 REMARK 3 3 2.1170 - 1.8507 0.98 2732 141 0.1987 0.2032 REMARK 3 4 1.8507 - 1.6821 0.99 2704 165 0.2270 0.2526 REMARK 3 5 1.6821 - 1.5619 0.98 2684 138 0.2839 0.2668 REMARK 3 6 1.5619 - 1.4700 0.97 2686 155 0.3566 0.3110 REMARK 3 7 1.4700 - 1.3966 0.96 2609 143 0.4086 0.3904 REMARK 3 8 1.3966 - 1.3359 0.95 2591 136 0.4590 0.4177 REMARK 3 9 1.3359 - 1.2845 0.94 2562 135 0.5129 0.4870 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.530 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.004 551 REMARK 3 ANGLE : 0.751 747 REMARK 3 CHIRALITY : 0.074 74 REMARK 3 PLANARITY : 0.004 98 REMARK 3 DIHEDRAL : 21.256 217 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6AT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25429 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.285 REMARK 200 RESOLUTION RANGE LOW (A) : 11.224 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 5.360 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 STARTING MODEL: 1KNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 3.0M (NH4)2SO4, PH 5.8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.23950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.23950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.20850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.42850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.20850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.42850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.23950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.20850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.42850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.23950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.20850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.42850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 135 LIES ON A SPECIAL POSITION. 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 MET A 8 REMARK 465 LYS A 9 REMARK 465 LYS A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 ALA A 17 REMARK 465 GLU A 18 REMARK 465 GLU A 19 REMARK 465 GLU A 20 REMARK 465 GLU A 21 REMARK 465 LYS A 75 REMARK 465 ASP A 76 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 62 73.65 -115.74 REMARK 500 CYS A 63 55.97 -142.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 6AT0 A 17 76 UNP P05205 HP1_DROME 17 76 DBREF 6AT0 P 5 10 PDB 6AT0 6AT0 5 10 SEQADV 6AT0 MET A 8 UNP P05205 INITIATING METHIONINE SEQADV 6AT0 LYS A 9 UNP P05205 EXPRESSION TAG SEQADV 6AT0 LYS A 10 UNP P05205 EXPRESSION TAG SEQADV 6AT0 HIS A 11 UNP P05205 EXPRESSION TAG SEQADV 6AT0 HIS A 12 UNP P05205 EXPRESSION TAG SEQADV 6AT0 HIS A 13 UNP P05205 EXPRESSION TAG SEQADV 6AT0 HIS A 14 UNP P05205 EXPRESSION TAG SEQADV 6AT0 HIS A 15 UNP P05205 EXPRESSION TAG SEQADV 6AT0 HIS A 16 UNP P05205 EXPRESSION TAG SEQADV 6AT0 PPN A 24 UNP P05205 TYR 24 ENGINEERED MUTATION SEQADV 6AT0 MET A 38 UNP P05205 LYS 38 ENGINEERED MUTATION SEQRES 1 A 69 MET LYS LYS HIS HIS HIS HIS HIS HIS ALA GLU GLU GLU SEQRES 2 A 69 GLU GLU GLU PPN ALA VAL GLU LYS ILE ILE ASP ARG ARG SEQRES 3 A 69 VAL ARG LYS GLY MET VAL GLU TYR TYR LEU LYS TRP LYS SEQRES 4 A 69 GLY TYR PRO GLU THR GLU ASN THR TRP GLU PRO GLU ASN SEQRES 5 A 69 ASN LEU ASP CYS GLN ASP LEU ILE GLN GLN TYR GLU ALA SEQRES 6 A 69 SER ARG LYS ASP SEQRES 1 P 6 GLN THR ALA ARG M3L SER HET PPN A 24 14 HET M3L P 9 12 HETNAM PPN PARA-NITROPHENYLALANINE HETNAM M3L N-TRIMETHYLLYSINE FORMUL 1 PPN C9 H10 N2 O4 FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 HOH *40(H2 O) HELIX 1 AA1 PRO A 49 ASN A 53 5 5 HELIX 2 AA2 CYS A 63 ARG A 74 1 12 SHEET 1 AA1 5 THR A 54 PRO A 57 0 SHEET 2 AA1 5 MET A 38 TRP A 45 -1 N LEU A 43 O THR A 54 SHEET 3 AA1 5 GLU A 23 ARG A 35 -1 N ILE A 30 O TYR A 42 SHEET 4 AA1 5 THR P 6 ARG P 8 -1 O ALA P 7 N PPN A 24 SHEET 5 AA1 5 LEU A 61 ASP A 62 -1 N ASP A 62 O THR P 6 LINK C GLU A 23 N PPN A 24 1555 1555 1.33 LINK C PPN A 24 N ALA A 25 1555 1555 1.33 LINK C ARG P 8 N M3L P 9 1555 1555 1.33 LINK C M3L P 9 N ASER P 10 1555 1555 1.33 LINK C M3L P 9 N BSER P 10 1555 1555 1.33 CRYST1 34.417 76.857 76.479 90.00 90.00 90.00 C 2 2 21 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 0.029055 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013075 0.00000