HEADER TRANSCRIPTION/PEPTIDE 12-JAN-16 5HJB TITLE AF9 YEATS IN COMPLEX WITH HISTONE H3 CROTONYLATION AT K9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN AF-9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: YEATS DOMAIN, UNP RESIDUES 1-138; COMPND 5 SYNONYM: ALL1-FUSED GENE FROM CHROMOSOME 9 PROTEIN,MYELOID/LYMPHOID COMPND 6 OR MIXED-LINEAGE LEUKEMIA TRANSLOCATED TO CHROMOSOME 3 PROTEIN,YEATS COMPND 7 DOMAIN-CONTAINING PROTEIN 3; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PEPTIDE OF HISTONE H3.1; COMPND 11 CHAIN: B; COMPND 12 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: MLLT3, AF9, YEATS3; 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: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS AF9 YEATS, HISTONE PEPTIDE, CROTONYLLYSINE, H3K9, TRANSCRIPTION- KEYWDS 2 PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.LI,D.ZHAO,H.P.GUAN,H.T.LI REVDAT 4 15-NOV-23 5HJB 1 REMARK REVDAT 3 08-NOV-23 5HJB 1 JRNL REMARK REVDAT 2 04-MAY-16 5HJB 1 JRNL REVDAT 1 20-APR-16 5HJB 0 JRNL AUTH Y.Y.LI,B.R.SABARI,T.PANCHENKO,H.WEN,D.ZHAO,H.P.GUAN,L.WAN, JRNL AUTH 2 H.HUANG,Z.TANG,Y.ZHAO,R.G.ROEDER,X.SHI,C.D.ALLIS,H.T.LI JRNL TITL MOLECULAR COUPLING OF HISTONE CROTONYLATION AND ACTIVE JRNL TITL 2 TRANSCRIPTION BY AF9 YEATS DOMAIN JRNL REF MOL.CELL V. 62 181 2016 JRNL REFN ISSN 1097-2765 JRNL PMID 27105114 JRNL DOI 10.1016/J.MOLCEL.2016.03.028 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.770 REMARK 3 FREE R VALUE TEST SET COUNT : 601 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 35.9255 - 4.2836 1.00 1441 151 0.1880 0.2108 REMARK 3 2 4.2836 - 3.4009 1.00 1395 133 0.2084 0.2802 REMARK 3 3 3.4009 - 2.9712 1.00 1378 151 0.2374 0.3197 REMARK 3 4 2.9712 - 2.6996 0.99 1334 166 0.2656 0.3287 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 82.32 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 : 0.010 1272 REMARK 3 ANGLE : 1.267 1712 REMARK 3 CHIRALITY : 0.055 176 REMARK 3 PLANARITY : 0.006 222 REMARK 3 DIHEDRAL : 19.205 770 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 5HJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6163 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 4TMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) POLYETHYLENE GLYCOL 4000, REMARK 280 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE, REMARK 280 3% MPD, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.45667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.22833 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 13.22833 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.45667 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: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 LYS A 90 78.37 -69.83 REMARK 500 PRO A 112 159.45 -49.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HJC RELATED DB: PDB REMARK 900 RELATED ID: 5HJD RELATED DB: PDB DBREF 5HJB A 1 138 UNP P42568 AF9_HUMAN 1 138 DBREF 5HJB B 3 10 UNP P68431 H31_HUMAN 4 11 SEQADV 5HJB SER A -1 UNP P42568 EXPRESSION TAG SEQADV 5HJB HIS A 0 UNP P42568 EXPRESSION TAG SEQRES 1 A 140 SER HIS MET ALA SER SER CYS ALA VAL GLN VAL LYS LEU SEQRES 2 A 140 GLU LEU GLY HIS ARG ALA GLN VAL ARG LYS LYS PRO THR SEQRES 3 A 140 VAL GLU GLY PHE THR HIS ASP TRP MET VAL PHE VAL ARG SEQRES 4 A 140 GLY PRO GLU HIS SER ASN ILE GLN HIS PHE VAL GLU LYS SEQRES 5 A 140 VAL VAL PHE HIS LEU HIS GLU SER PHE PRO ARG PRO LYS SEQRES 6 A 140 ARG VAL CYS LYS ASP PRO PRO TYR LYS VAL GLU GLU SER SEQRES 7 A 140 GLY TYR ALA GLY PHE ILE LEU PRO ILE GLU VAL TYR PHE SEQRES 8 A 140 LYS ASN LYS GLU GLU PRO ARG LYS VAL ARG PHE ASP TYR SEQRES 9 A 140 ASP LEU PHE LEU HIS LEU GLU GLY HIS PRO PRO VAL ASN SEQRES 10 A 140 HIS LEU ARG CYS GLU LYS LEU THR PHE ASN ASN PRO THR SEQRES 11 A 140 GLU ASP PHE ARG ARG LYS LEU LEU LYS ALA SEQRES 1 B 8 THR LYS GLN THR ALA ARG KCR SER MODRES 5HJB KCR B 9 LYS MODIFIED RESIDUE HET KCR B 9 14 HETNAM KCR N-6-CROTONYL-L-LYSINE FORMUL 2 KCR C10 H18 N2 O3 FORMUL 3 HOH *16(H2 O) HELIX 1 AA1 GLY A 38 SER A 42 5 5 HELIX 2 AA2 THR A 128 LYS A 137 1 10 SHEET 1 AA1 4 TYR A 71 GLY A 77 0 SHEET 2 AA1 4 HIS A 30 ARG A 37 -1 N TRP A 32 O GLU A 75 SHEET 3 AA1 4 ALA A 6 VAL A 19 -1 N GLN A 18 O ASP A 31 SHEET 4 AA1 4 VAL A 114 ASN A 125 -1 O PHE A 124 N VAL A 7 SHEET 1 AA2 4 LYS A 63 CYS A 66 0 SHEET 2 AA2 4 VAL A 48 HIS A 54 -1 N VAL A 51 O CYS A 66 SHEET 3 AA2 4 PHE A 81 PHE A 89 -1 O GLU A 86 N VAL A 52 SHEET 4 AA2 4 LYS A 97 LEU A 104 -1 O TYR A 102 N LEU A 83 LINK C ARG B 8 N KCR B 9 1555 1555 1.33 LINK C KCR B 9 N SER B 10 1555 1555 1.33 CISPEP 1 GLU A 26 GLY A 27 0 -28.62 CISPEP 2 PRO A 69 PRO A 70 0 -14.49 CISPEP 3 GLU A 94 PRO A 95 0 -6.42 CRYST1 97.595 97.595 39.685 90.00 90.00 120.00 P 32 2 1 6 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 0.010246 0.005916 0.000000 0.00000 SCALE2 0.000000 0.011832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025198 0.00000