HEADER TRANSCRIPTION 03-AUG-19 6KN5 TITLE CRYSTAL STRUCTURE OF AFF4 C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AF4/FMR2 FAMILY MEMBER 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALL1-FUSED GENE FROM CHROMOSOME 5Q31 PROTEIN,PROTEIN AF- COMPND 5 5Q31,MAJOR CDK9 ELONGATION FACTOR-ASSOCIATED PROTEIN; 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 GENE: AFF4, AF5Q31, MCEF, HSPC092; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AFF4, HISTONE ACETYLATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR L.J.CHEN,W.S.YANG,R.M.XU REVDAT 2 23-MAR-22 6KN5 1 REMARK REVDAT 1 08-JUL-20 6KN5 0 JRNL AUTH Y.GAO,L.CHEN,Y.HAN,F.WU,W.S.YANG,Z.ZHANG,T.HUO,Y.ZHU,C.YU, JRNL AUTH 2 H.KIM,M.LEE,Z.TANG,K.PHILLIPS,B.HE,S.Y.JUNG,Y.SONG,B.ZHU, JRNL AUTH 3 R.M.XU,Q.FENG JRNL TITL ACETYLATION OF HISTONE H3K27 SIGNALS THE TRANSCRIPTIONAL JRNL TITL 2 ELONGATION FOR ESTROGEN RECEPTOR ALPHA. JRNL REF COMMUN BIOL V. 3 165 2020 JRNL REFN ESSN 2399-3642 JRNL PMID 32265480 JRNL DOI 10.1038/S42003-020-0898-0 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14444 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1445 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 46.9350 - 4.7385 1.00 1403 156 0.2338 0.2830 REMARK 3 2 4.7385 - 3.7616 1.00 1313 147 0.2081 0.2656 REMARK 3 3 3.7616 - 3.2862 1.00 1307 144 0.2473 0.2883 REMARK 3 4 3.2862 - 2.9858 1.00 1304 146 0.2681 0.3202 REMARK 3 5 2.9858 - 2.7718 1.00 1286 142 0.2746 0.2958 REMARK 3 6 2.7718 - 2.6084 1.00 1279 142 0.2815 0.2886 REMARK 3 7 2.6084 - 2.4778 1.00 1286 144 0.2934 0.3133 REMARK 3 8 2.4778 - 2.3699 1.00 1266 140 0.3020 0.3382 REMARK 3 9 2.3699 - 2.2787 1.00 1256 140 0.2862 0.3470 REMARK 3 10 2.2787 - 2.2001 1.00 1299 144 0.3015 0.3560 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.01 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 1873 REMARK 3 ANGLE : 0.719 2525 REMARK 3 CHIRALITY : 0.312 279 REMARK 3 PLANARITY : 0.004 319 REMARK 3 DIHEDRAL : 25.604 707 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 6KN5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97845 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14447 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.94600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM DIHYDROGEN PHOSPHATE, POTASSIUM REMARK 280 MONOHYDROGEN PHOSPHATE, 2-(N-MORPHOLINO)ETHANESULFONIC ACID, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 20.53100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.70850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.55850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 93.70850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.53100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.55850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.53100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.55850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 93.70850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.55850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.53100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.70850 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: 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 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 A 898 REMARK 465 SER A 899 REMARK 465 LYS A 900 REMARK 465 PRO A 901 REMARK 465 GLY A 1047 REMARK 465 SER A 1048 REMARK 465 LYS A 1049 REMARK 465 ALA A 1050 REMARK 465 VAL A 1051 REMARK 465 GLY A 1052 REMARK 465 MET A 1053 REMARK 465 PRO A 1054 REMARK 465 SER A 1055 REMARK 465 PRO A 1056 REMARK 465 VAL A 1057 REMARK 465 SER A 1058 REMARK 465 PRO A 1059 REMARK 465 LYS A 1060 REMARK 465 LEU A 1061 REMARK 465 SER A 1062 REMARK 465 PRO A 1063 REMARK 465 GLY A 1064 REMARK 465 ASN A 1065 REMARK 465 SER A 1066 REMARK 465 GLY A 1067 REMARK 465 ASN A 1068 REMARK 465 TYR A 1069 REMARK 465 SER A 1070 REMARK 465 SER A 1071 REMARK 465 GLY A 1072 REMARK 465 ALA A 1073 REMARK 465 SER A 1074 REMARK 465 SER A 1075 REMARK 465 ALA A 1076 REMARK 465 SER A 1077 REMARK 465 ALA A 1078 REMARK 465 SER A 1079 REMARK 465 GLY A 1080 REMARK 465 LEU A 1161 REMARK 465 ILE A 1162 REMARK 465 SER A 1163 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 TYR A1036 31.40 -145.94 REMARK 500 ASN A1038 -17.17 75.67 REMARK 500 SER A1039 -55.64 -122.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KN5 A 899 1163 UNP Q9UHB7 AFF4_HUMAN 899 1163 SEQADV 6KN5 GLY A 898 UNP Q9UHB7 EXPRESSION TAG SEQRES 1 A 266 GLY SER LYS PRO ARG ARG THR LYS LEU VAL PHE ASP ASP SEQRES 2 A 266 ARG ASN TYR SER ALA ASP HIS TYR LEU GLN GLU ALA LYS SEQRES 3 A 266 LYS LEU LYS HIS ASN ALA ASP ALA LEU SER ASP ARG PHE SEQRES 4 A 266 GLU LYS ALA VAL TYR TYR LEU ASP ALA VAL VAL SER PHE SEQRES 5 A 266 ILE GLU CYS GLY ASN ALA LEU GLU LYS ASN ALA GLN GLU SEQRES 6 A 266 SER LYS SER PRO PHE PRO MET TYR SER GLU THR VAL ASP SEQRES 7 A 266 LEU ILE LYS TYR THR MET LYS LEU LYS ASN TYR LEU ALA SEQRES 8 A 266 PRO ASP ALA THR ALA ALA ASP LYS ARG LEU THR VAL LEU SEQRES 9 A 266 CYS LEU ARG CYS GLU SER LEU LEU TYR LEU ARG LEU PHE SEQRES 10 A 266 LYS LEU LYS LYS GLU ASN ALA LEU LYS TYR SER LYS THR SEQRES 11 A 266 LEU THR GLU HIS LEU LYS ASN SER TYR ASN ASN SER GLN SEQRES 12 A 266 ALA PRO SER PRO GLY LEU GLY SER LYS ALA VAL GLY MET SEQRES 13 A 266 PRO SER PRO VAL SER PRO LYS LEU SER PRO GLY ASN SER SEQRES 14 A 266 GLY ASN TYR SER SER GLY ALA SER SER ALA SER ALA SER SEQRES 15 A 266 GLY SER SER VAL THR ILE PRO GLN LYS ILE HIS GLN MET SEQRES 16 A 266 ALA ALA SER TYR VAL GLN VAL THR SER ASN PHE LEU TYR SEQRES 17 A 266 ALA THR GLU ILE TRP ASP GLN ALA GLU GLN LEU SER LYS SEQRES 18 A 266 GLU GLN LYS GLU PHE PHE ALA GLU LEU ASP LYS VAL MET SEQRES 19 A 266 GLY PRO LEU ILE PHE ASN ALA SER ILE MET THR ASP LEU SEQRES 20 A 266 VAL ARG TYR THR ARG GLN GLY LEU HIS TRP LEU ARG GLN SEQRES 21 A 266 ASP ALA LYS LEU ILE SER FORMUL 2 HOH *33(H2 O) HELIX 1 AA1 SER A 914 LEU A 932 1 19 HELIX 2 AA2 ASP A 934 ASN A 959 1 26 HELIX 3 AA3 PRO A 966 LYS A 982 1 17 HELIX 4 AA4 THR A 992 LYS A 1018 1 27 HELIX 5 AA5 LYS A 1018 LYS A 1033 1 16 HELIX 6 AA6 PRO A 1086 SER A 1117 1 32 HELIX 7 AA7 GLN A 1120 GLY A 1132 1 13 HELIX 8 AA8 ILE A 1140 LYS A 1160 1 21 CRYST1 41.062 71.117 187.417 90.00 90.00 90.00 I 21 21 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 0.024353 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005336 0.00000